OpenAlea

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

Funding: Agropolis foundation (Contractors for Virtual Plants: CIRAD and Inria from 2009 to 2013)

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, ...

Fruit3D

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

Funding: Agropolis foundation (Contractor for Virtual Plants: INRA, from 2009 to 2012)

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. 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.

Funding: Agropolis foundation (Contractor for Virtual Plants: CIRAD, From 2009 to 2012)

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 AGAP, UMR LEPSE (Montpellier), UMR PIAF (INRA Clermont Ferrand), UMR URP3F (Inra Lusignan), EPI Galaad (Inria Sophia Antipolis), EPI Imagine (Inria Grenoble). University of Helsinki, Finland.

Agropolis computational plant seminar

Participants : Yann Guédon, Christine Granier [INRA, LEPSE] , Soazig Guyomarc'H [Montpellier 2 University, DIADE] .

Funding: Agropolis foundation (Contractor for Virtual Plants: CIRAD. From 2008 to 2012)

In the context of the creation of a world-level pole on plant science in the région Languedoc-Roussillon, we created a monthly seminar on plant modeling and its applications. 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.

Rhizopolis

Participants : Frédéric Boudon, Christophe Godin, Yann Guédon, Christophe Pradal.

Funding: Agropolis foundation (Contractor for Virtual Plants: INRA, from 2011 to 2013)

Rhizopolis is a multidisciplinary project on the biology and ecology of the plant root that addresses the broad roles of this organ in mineral nutrient and water acquisition. The consortium addresses central issues of root development, that are operationally divided into 3 work packages.