A rule-based functional-structural model of rice considering source and sink functions

As a first step towards a generic genotype-phenotype model of rice, we present here a model of the growth and morphology of rice in combination with ecophysiological processes using the technique of functional-structural plant modelling (FSPM) and the interactive modelling platform GroIMP along with the graph-based Relational Growth Grammar formalism. The model constitutes a simple yet functionally coherent phenotype model of rice, consisting of a set of morphogenetic RGG rules describing an “average” developmental course and final morphology, partially linking yield traits to processes (tiller and grain number, stem length, grain filling rate, grain weight)

Comparison of Pruning Regimes for Stone Pine (Pinus pinea L.) Using a Functional- Structural Plant Model

Functional-Structural Plant Models (FSPM) are becoming important tools for modeling the structure and growth of plants, including complex organisms like trees. These models combine the advantages of empirical, mechanistic, and structural models to simulate the growth of individual plant structures (branches, buds, leaves, etc.). This approach enables realistic evaluation of the plant’s response– including changes in structure and growth to different environmental conditions. We demonstrate the potential use of these models to evaluate individual tree growth under different management regimes (pruning). The data used in this study was obtained from 3-D measurements taken with a FASTRAK Polhemus digitizer, with specific attention given to bud creation and branching. Each branch segment was analyzed to estimate its age, enabling us to document annual structural changes. We use the XL programming language and a GroIMP environment to simulate and compare different pruning scenarios

Realization and Extension of the Xfrog Approach for Plant Modelling in the Graph-Grammar Based Language XL

Two well-known approaches for modelling virtual vegetation are grammar-based methods (L-systems) and the Xfrog method, which is based on graph transformations expanding "multiplier" nodes. We show that both approaches can be unified in the framework of "relational growth grammars", a variant of parallel graph grammars. We demonstrate this possibility and the synergistic benefits of the combination of both methods at simple plant models which were processed using our open-source software GroIMP

Parallel Graph Grammars with Instantiation Rules Allow Efficient Structural Factorization of Virtual Vegetation

Parallel rewriting of typed attributed graphs, based on the single-pushout approach extended by connection transformations, serves as the backbone of the multi-paradigm language XL, which is widely used in functional-structural plant modelling. XL allows to define instantiation rules, which enable an instancing of graphs at runtime for frequently occurring substructures, e.g., in 3-d models of botanical trees. This helps to save computer memory during complex simulations of vegetation structure. Instantiation rules can be called recursively and with references to graph nodes, thus providing a unifying formal framework for various concepts from the literature: object instancing, structural factorization, Xfrog multiplier nodes, L-systems with interpretation. We give simple examples and measure the computation time for an idealized growing virtual plant, taken from the GreenLab model, in its implementation with instantiation rules in XL, compared to a version without instantiation rules

FSPM-P: towards a general functional-structural plant model for robust and comprehensive model development

In the last decade, functional-structural plant modelling (FSPM) has become a more widely accepted paradigm in crop and tree production, as 3D models for the most important crops have been proposed. Given the wider portfolio of available models, it is now appropriate to enter the next level in FSPM development, by introducing more efficient methods for model development. This includes the consideration of model reuse (by modularisation), combination and comparison, and the enhancement of existing models. To facilitate this process, standards for design and communication need to be defined and established. We present a first step towards an efficient and general, i.e., not speciesspecific FSPM, presently restricted to annual or bi-annual plants, but with the potential for extension and further generalization. Model structure is hierarchical and object-oriented, with plant organs being the base-level objects and plant individual and canopy the higher-level objects. Modules for the majority of physiological processes are incorporated, more than in other platforms that have a similar aim (e.g., photosynthesis, organ formation and growth). Simulation runs with several general parameter sets adopted from the literature show that the present prototypewas able to reproduce a plausible output range for different crops (rapeseed, barley, etc.) in terms of both the dynamics and final values (at harvest time) of model state variables such as assimilate production, organ biomass, leaf area and architecture

Engineering model transformations with transML

The final publication is available at Springer via http://dx.doi.org/10.1007%2Fs10270-011-0211-2Model transformation is one of the pillars of model-driven engineering (MDE). The increasing complexity of systems and modelling languages has dramatically raised the complexity and size of model transformations as well. Even though many transformation languages and tools have been proposed in the last few years, most of them are directed to the implementation phase of transformation development. In this way, even though transformations should be built using sound engineering principles—just like any other kind of software—there is currently a lack of cohesive support for the other phases of the transformation development, like requirements, analysis, design and testing. In this paper, we propose a unified family of languages to cover the life cycle of transformation development enabling the engineering of transformations. Moreover, following an MDE approach, we provide tools to partially automate the progressive refinement of models between the different phases and the generation of code for several transformation implementation languages.This work has been sponsored by the Spanish Ministry of Science and Innovation with project METEORIC (TIN2008-02081), and by the R&D program of the Community of Madrid with projects “e-Madrid" (S2009/TIC-1650). Parts of this work were done during the research stays of Esther and Juan at the University of York, with financial support from the Spanish Ministry of Science and Innovation (grant refs. JC2009-00015, PR2009-0019 and PR2008-0185)