OpenAlea: a visual programming and component-based software platform for plant modelling

Christophe Pradal; Samuel Dufour-Kowalski; Frédéric Boudon; Christian Fournier; Christophe Godin

doi:10.1071/FP08084

RESEARCH ARTICLE (Open Access)

OpenAlea: a visual programming and component-based software platform for plant modelling

Christophe Pradal ^A ^D , Samuel Dufour-Kowalski ^B , Frédéric Boudon ^A , Christian Fournier ^C and Christophe Godin ^B

+ Author Affiliations

- Author Affiliations

^A CIRAD, UMR DAP and INRIA, Virtual Plants, TA A-96/02, 34398 Montpellier Cedex 5, France.

^B INRIA, UMR DAP, Virtual Plants, TA A-96/02, 34398 Montpellier Cedex 5, France.

^C INRA, UMR 759 LEPSE, 2 place Viala, 34060 Montpellier cedex 01, France.

^D Corresponding author. Email: christophe.pradal@cirad.fr

This paper originates from a presentation at the 5th International Workshop on Functional–Structural Plant Models, Napier, New Zealand, November 2007.

Functional Plant Biology 35(10) 751-760 https://doi.org/10.1071/FP08084
Submitted: 18 March 2008 Accepted: 29 July 2008 Published: 11 November 2008

Abstract

The development of functional–structural plant models requires an increasing amount of computer modelling. All these models are developed by different teams in various contexts and with different goals. Efficient and flexible computational frameworks are required to augment the interaction between these models, their reusability, and the possibility to compare them on identical datasets. In this paper, we present an open-source platform, OpenAlea, that provides a user-friendly environment for modellers, and advanced deployment methods. OpenAlea allows researchers to build models using a visual programming interface and provides a set of tools and models dedicated to plant modelling. Models and algorithms are embedded in OpenAlea ‘components’ with well defined input and output interfaces that can be easily interconnected to form more complex models and define more macroscopic components. The system architecture is based on the use of a general purpose, high-level, object-oriented script language, Python, widely used in other scientific areas. We present a brief rationale that underlies the architectural design of this system and we illustrate the use of the platform to assemble several heterogeneous model components and to rapidly prototype a complex modelling scenario.

Additional keywords: dataflow, interactive modelling, light interception, plant modeling, software architecture.

Acknowledgements

The authors thank Mrs and Mr Hopkins for editorial help, and the two anonymous reviewers for their constructive criticism. This research has been supported by the developer community of OpenAlea, by grants from INRIA, CIRAD, and INRA (Réseau Ecophysiologique de l’Arbre), and by the ANR project NatSim.

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