Towards aspect-oriented functional-structural plant modelling

Mikolaj Cieslak1,2, Alla N. Seleznyova2, Przemyslaw Prusinkiewicz3, and Jim Hanan1
1 University of Queensland
2 New Zealand Institute for Plant and Food Research
3 University of Calgary

Abstract

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.

Reference

Mikolaj Cieslak, Alla N. Seleznyova, Przemyslaw Prusinkiewicz, and Jim Hanan. Towards aspect-oriented functional-structural plant modelling. Annals of Botany 108(6), pp. 1025-1041, 2011.

Download PDF from the publisher's site (600kb). You can also download the L-system kiwifruit model described in the paper (ZIP archive, 20 kb; you will need L-studio or VLAB to run the model.)