Virtual Plants

The Virtual Plants is an INRIA project-team, joint with CIRAD and INRA. It is located at UMR AGAP, Montpellier, France. The long-term focus of the project is to study plant development and its control by genetic processes.

Motivation: Plants are branching living organisms that develop throughout their lifetimes. Organs are created by small embryogenetic regions at the tip of each axis, called apical meristems . In the project Virtual Plants, we are interested in studying plant apical meristem functioning and development. We believe that a detailed analysis of apical meristem processes, based on advanced mathematical and computational methods and tools, will lead us to get a deeper and better understanding of plant development.

Biological keywords: Plant development, branching systems, plant architecture analysis, plant geometry and topology, branching patterns, meristems, growth, vegetal tissues, hormones, auxine fluxes, meristem physiological states, shoots, roots.

Mathematical keywords: Developmental processes, dynamic systems with dynamic structures (DS)2, stochastic processes, Markov processes, transport processes, partial differential equations, mechanical models, L-systems, MGS, plant and fractals, tree-graph comparison, self-similarity in trees, tree compression, multiscale structures and analysis, 3D imaging.

Research 

The general aim of Virtual Plants is to design a computational approach of plant development to better understand the complex interaction of physical, physiological and genetic mechanisms that control plant morphogenesis. To address this question, we aim to build up an integrated picture of meristem development at different spatial and temporal scales by bringing together knowledge coming from plant architecture at macroscopic scales and from developmental biology at cellular and molecular scales. This is carried out by developing a research programme that integrates mathematical, computer science and biological perspectives at complementary scales, from cellular to whole plant scale.

At a macroscopic level, recent progresses in phenotyping of plant structure and development (automation, high-thoughput data, new 3D sensors, etc.) require the conception of new methodological pipelines from sensor outputs to pattern modeling. Our general aim is to infer meristem functioningfrom the complex structures they produce over time. This analysis is carried out at different spatial and temporal scales.

At a microscopic level, we intend to exploit the recent spectacular scientific and technological progresses in developmental biology and genetics in order to understand how the genetic, biophysical and physiological processes control morphogenesis at meristem level.

The team develops a modular and open-source software platform, OpenAleaLab, that integrates various components to model and simulate plant development. OpenAleaLab is a component-based platform embedded in the programming language Python. It offers a plug-in mechanism that makes it possible to easily add and share new models and components.