Journal Article

Towards aspect-oriented functional–structural plant modelling

Mikolaj Cieslak, Alla N. Seleznyova, Przemyslaw Prusinkiewicz and Jim Hanan

in Annals of Botany

Published on behalf of The Annals of Botany Company

Volume 108, issue 6, pages 1025-1041
Published in print October 2011 | ISSN: 0305-7364
Published online July 2011 | e-ISSN: 1095-8290 | DOI: http://dx.doi.org/10.1093/aob/mcr121
Towards aspect-oriented functional–structural plant modelling

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  • Ecology and Conservation
  • Evolutionary Biology
  • Plant Sciences and Forestry

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Background and Aims

Functional–structural plant models (FSPMs) are used to integrate knowledge and test hypotheses of plant behaviour, and to aid in the development of decision support systems. A significant amount of effort is being put into providing a sound methodology for building them. Standard techniques, such as procedural or object-oriented programming, are not suited for clearly separating aspects of plant function that criss-cross between different components of plant structure, which makes it difficult to reuse and share their implementations. The aim of this paper is to present an aspect-oriented programming approach that helps to overcome this difficulty.

Methods

The L-system-based plant modelling language L+C was used to develop an aspect-oriented approach to plant modelling based on multi-modules. Each element of the plant structure was represented by a sequence of L-system modules (rather than a single module), with each module representing an aspect of the element's function. Separate sets of productions were used for modelling each aspect, with context-sensitive rules facilitated by local lists of modules to consider/ignore. Aspect weaving or communication between aspects was made possible through the use of pseudo-L-systems, where the strict-predecessor of a production rule was specified as a multi-module.

Key Results

The new approach was used to integrate previously modelled aspects of carbon dynamics, apical dominance and biomechanics with a model of a developing kiwifruit shoot. These aspects were specified independently and their implementation was based on source code provided by the original authors without major changes.

Conclusions

This new aspect-oriented approach to plant modelling is well suited for studying complex phenomena in plant science, because it can be used to integrate separate models of individual aspects of plant development and function, both previously constructed and new, into clearly organized, comprehensive FSPMs. In a future work, this approach could be further extended into an aspect-oriented programming language for FSPMs.

Keywords: L-system; aspect-oriented programming; Actinidia deliciosa (kiwifruit); functional–structural plant model; plant architecture; carbon dynamics; biomechanics; hormone transport

Journal Article.  10985 words.  Illustrated.

Subjects: Ecology and Conservation ; Evolutionary Biology ; Plant Sciences and Forestry

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