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. Work comprises the development of standard data structures, deployment tools, documentation, training, software engineering, user interface, interfaces with other platform, ...

Agropolis computational plant seminar

Participants : Yann Guédon, Thierry Fourcaud [CIRAD, AMAP] , Christine Granier [INRA, LEPSE] , Soazig Guyomarc'H [Montpellier 2 University, DIADE] , Laurent Laplaze [IRD, DIADE] .

Funding: Agropolis foundation (Contractor for Virtual Plants: CIRAD. From 2013 to 2016)

In the context of the creation of a world-level pole on plant science in the region Languedoc-Roussillon, we created a monthly seminar on plant modeling and its applications. The seminar is organized by Yann Guédon, Thierry Fourcaud (CIRAD, AMAP), Christine Granier (INRA, LESPE), Soazig Guyomarc'h (Montpellier 2 University, DIADE) and Laurent Laplaze (IRD, DIADE) with the support of Agropolis International and Agropolis Foundation.

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 project gathers the competences of plant modelers, physicists and ecophysiologists for developing a virtual tomato model. The model contains the geometrical description of a growing fruit, physical and biological laws involved in tissue differentiation and cell growth, physiological models (for sugar and hormone transfers) and mechanical model. 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.

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 adresses central issues such as the coupling of membrane transport activity and structure-function relationships in roots and root symbioses, the integration of root-soil interactions in the rhizosphere at the whole root system level, and the development of key tools for imaging root development. Virtual Plants is mainly involved in the developement of a software for automatically reconstructing root systems from 2D images.

Partners: DAR Team, UMR AGAP, UMR BPMC and UMR LEPSE (Montpellier).

RhizoScanHT

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

Funding: Labex Numev (Contractor for Virtual Plants: UM2, from 2013 to 2014)

In this project, we extend the pipeline of 2D root system reconstruction developed in the project RhizoPolis to deal with high-thoughput data. For this we develop the project in two directions: i) make the pipeline software components more robust to various acquisition conditions and root system complexities ii) use techniques coming from the big data community to upscale the indexing and reconstruction methods.

Partners: Zenith Inria Project Team, UMR AGAP, UMR BPMC and UMR LEPSE (Montpellier).