Section: Partnerships and Cooperations

National Grants

Agropolis computational plant seminar

Participants : Yann Guédon, Christine Granier [INRA, LEPSE] , Laurent Laplaze [IRD, DIAPC] .

Funding: Agropolis foundation (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 2011 two-day workshop was devoted to Models at whole plant scale. The invited speakers were Winfried Kurth (University of Göttingen), Mathieu Javaux (Université Catholique de Louvain), Yann Guédon, Renaud Bastien (INRA, PIAF), Frédéric Mothe (INRA, LERFoB), Annikki Mäkelä (University of Helsinki), David Da Silva (UC Davis), Michaël Chelle (INRA, EGC), Jochem B. Evers (Wageningen University), Brian Enquist (University of Arizona, Tucson), François Tardieu (INRA, LEPSE). The seminar is organized by Yann Guédon, Christine Granier (INRA, LESPE) and Soazig Guyomarc'h (Montpellier 2 University, DIADE) with the support of Agropolis International and Agropolis Foundation.

OpenAlea

Participants : Christophe Pradal, Christophe Godin, Christian Fournier [INRA, LEPSE] .

Funding: Agropolis foundation (Contractors for Virtual Plants: CIRAD and INRIA from 2009 to 2012)

The aim of this project is to foster the development and the national and international diffusion of the platform OpenAlea. This opensource platform provides an easy-to-use environment for plant modelers through a visual programming interface to efficiently use and combine models or computational methods from different scientific fields in order to represent, analyze 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, ...

vTissue

Participants : Eric Moscardi, Christophe Pradal, Christophe Godin, Grégoire Malandain [INRIA, Asclepios] .

Funding: INRIA ADT (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 modeling 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

Phenomena

Participants : Christophe Pradal, Christian Fournier [INRA, LEPSE] , Benoit de Solan [Arvalis/INRA, Avignon] , Frédéric Baret [INRA, UMMAH] , Elmer Ccopa-Rivero [INRA, UMMAH] , Bruno Andrieu [INRA, EGC] , Michel Chelle [INRA, EGC] .

Funding: Agropolis foundation (Contractors for Virtual Plants: CIRAD (INRIA sub-contractor) from 2010 to 2012)

The aim of this project is to combine a 4D plant model with a functioning model as a support to improve field high throughput phenotyping with remote sensors. This is a critical need to enhance interpretation of large amount of genotypic data made available by sequencing methods in constant improvement. Collecting more frequent and more accurate plant and stand measurements may lead to a better characterization of cultivar response to stresses.

Plant breeding appears to be a major component in the way to solve the new challenges that agriculture in Mediterranean areas is facing. New techniques allowing to access specific traits of cultivars have to be developed based on non destructive and rapid measurements such as those offered by close range remote sensing known as proxidetection.

This work is based on two existing models, the NEMA model for nitrogen dynamic between leaves and the Alinea.ADEL architectural model. Implementation use the modeling platform OpenAlea, dedicated to functional structural modeling of plants. The coupled model is then be used to simulate reflectance and gap fraction with a radiative transfer model (Baret et al., 2007).

Fruit3D

Participants : Mik Cieslak, Frédéric Boudon, Christophe Godin, Nadia Bertin [PSH, Avignon] .

Funding: Agropolis foundation (Contractor for Virtual Plants: INRA, from 2009 to 2011)

The aim of this project is to develop a virtual tomato that contains the geometrical description of a growing fruit, physiological models (for sugar and hormone transfers) and mechanical model. The project gathers the competences of plant modelers, physicists and ecophysiologists. Physical and biological laws involved in tissue differentiation and cell growth, in relation to fruit growth and compartmentalization, and a number of related traits of quality (e.g. size, composition and texture) are modeled 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.

PlantScan3D

Participants : Frédéric Boudon, Chakkrit Preuksakarn, Jean-Baptiste Durand, Christophe Godin, Christian Fournier [INRA, LEPSE] .

Funding: Agropolis foundation (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 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 develop methodologies for the automation of numerical 3D acquisition of vegetal structures of different sizes, and new methods for the reconstruction of parsimonious geometrical and structural models usable in agronomic 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.

GeneShape

Participants : Jérôme Chopard, Michael Walker, Etienne Farcot, 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 also have 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 constraints, different number of cells, different timing) to create morphologically similar shapes.

Partners: ENS-Lyon; P. Lemaire, CRBM, Montpellier.