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

Functional Plant Biology : FPB
Christophe PradalChristophe Godin

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 rapid...Continue Reading

References

May 5, 2005·The New Phytologist·Christophe Godin, Herve Sinoquet

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Citations

Aug 18, 2009·Annals of Botany·Florence Chaubert-PereiraYann Guédon
Mar 3, 2010·Annual Review of Plant Biology·Vijay ChickarmaneElliot M Meyerowitz
Mar 13, 2013·Proceedings of the National Academy of Sciences of the United States of America·Mikaël LucasMalcolm J Bennett
Aug 1, 2015·Rice·Nourollah AhmadiJian Xu
Dec 6, 2016·Frontiers in Plant Science·Mikolaj CieslakNadia Bertin
May 31, 2017·Frontiers in Plant Science·Amy Marshall-ColonXin-Guang Zhu
Feb 13, 2018·Annals of Botany·Andrea SchnepfHarry Vereecken
Dec 1, 2008·Functional Plant Biology : FPB·Reinhard HemmerlingGerhard Buck-Sorlin
Dec 10, 2009·Journal of Experimental Botany·J VosP H B de Visser
Aug 16, 2011·Journal of Experimental Botany·Olivier TaugourdeauYann Guédon
Feb 12, 2011·Plant, Cell & Environment·Mikaël LucasMalcolm J Bennett
Mar 1, 2012·Journal of Experimental Botany·Dirk De VosGerrit T S Beemster
Sep 10, 2014·Proceedings of the National Academy of Sciences of the United States of America·Yin Hoon ChewAndrew J Millar
Sep 22, 2016·Proceedings of the National Academy of Sciences of the United States of America·Nathan MellorMarkus R Owen
Oct 7, 2016·Interface Focus·John A FozardOliver E Jensen
May 20, 2017·Frontiers in Plant Science·Dirk De VosJan Broeckhove
Aug 24, 2018·Journal of Experimental Botany·Tsu-Wei ChenFrançois Tardieu
Jan 8, 2019·Journal of Experimental Botany·Andrew J MillarTomasz Zielinski
Sep 29, 2020·Frontiers in Plant Science·Ying-Tsui WangGerrit Hoogenboom
Dec 4, 2014·Annals of Botany·Risto SievänenEero Nikinmaa
Feb 26, 2016·Journal of Integrative Plant Biology·Christopher N ToppZhengbin Liu
Jun 5, 2020·Journal of Experimental Botany·Marion GauthierBruno Andrieu
Dec 29, 2019·Bioinformatics·Soumitra Pal, Teresa M Przytycka
Jul 5, 2011·Annals of Botany·Mikolaj CieslakJim Hanan

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