An approach to multiscale modelling with graph grammars

Ong, Yongzhi; Streit, Katarína; Henke, M.; Kurth, Winfried

doi:10.1093/aob/mcu155

Cited by 17 publications

(7 citation statements)

References 41 publications

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“…Independently, Godin and Caraglio ( Godin and Caraglio, 1998 ) have introduced a multiscale formalism, the MTG, to be able to encode any type of plant architecture data at different spatial and temporal scales. While a large community has adopted this formalism, the use of multiscale modeling to simulate the dynamic development of plants is quite recent ( Boudon et al, 2012 ; Ong et al, 2014 ).…”

Section: Ontologies For Plant Morphologymentioning

confidence: 99%

Reshaping Plant Biology: Qualitative and Quantitative Descriptors for Plant Morphology

et al. 2017

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An emerging challenge in plant biology is to develop qualitative and quantitative measures to describe the appearance of plants through the integration of mathematics and biology. A major hurdle in developing these metrics is finding common terminology across fields. In this review, we define approaches for analyzing plant geometry, topology, and shape, and provide examples for how these terms have been and can be applied to plants. In leaf morphological quantifications both geometry and shape have been used to gain insight into leaf function and evolution. For the analysis of cell growth and expansion, we highlight the utility of geometric descriptors for understanding sepal and hypocotyl development. For branched structures, we describe how topology has been applied to quantify root system architecture to lend insight into root function. Lastly, we discuss the importance of using morphological descriptors in ecology to assess how communities interact, function, and respond within different environments. This review aims to provide a basic description of the mathematical principles underlying morphological quantifications.

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Section: Ontologies For Plant Morphologymentioning

confidence: 99%

Reshaping Plant Biology: Qualitative and Quantitative Descriptors for Plant Morphology

et al. 2017

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“…For example, as established concepts are frequently adjusted to provide new approaches in modeling studies, L-system was an open tool and concept (Prusinkiewicz and Lindenmayer, 1990 ) with a multi-modules system for integrating previous modeled aspects of carbon dynamics (Allen et al, 2005 ), apical dominance (Prusinkiewicz et al, 2009 ), and biomechanics (Taylor-Hell, 2005 ; Prusinkiewicz et al, 2007 ) into a well-structured FSPM (Cieslak et al, 2011 ). This is illustrated in the study of Ong et al ( 2014 ), where the programming language XL and GroIMP platform have been used to explore models of plant growth that allow appropriately the use of several structural scales in plant description, highlighting the multi-scalar potentials of FSPMs. The result pointed out 3 contrasting models that show the way for combining information from various scales in the models.…”

Section: Functional–structural Plant Models Amenable To Cross Disciplines and Scalesmentioning

confidence: 99%

Functional–Structural Plant Models Mission in Advancing Crop Science: Opportunities and Prospects

et al. 2021

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Functional–structural plant models (FSPMs) have been evolving for over 2 decades and their future development, to some extent, depends on the value of potential applications in crop science. To date, stabilizing crop production by identifying valuable traits for novel cultivars adapted to adverse environments is topical in crop science. Thus, this study will examine how FSPMs are able to address new challenges in crop science for sustainable crop production. FSPMs developed to simulate organogenesis, morphogenesis, and physiological activities under various environments and are amenable to downscale to the tissue, cellular, and molecular level or upscale to the whole plant and ecological level. In a modeling framework with independent and interactive modules, advanced algorithms provide morphophysiological details at various scales. FSPMs are shown to be able to: (i) provide crop ideotypes efficiently for optimizing the resource distribution and use for greater productivity and less disease risk, (ii) guide molecular design breeding via linking molecular basis to plant phenotypes as well as enrich crop models with an additional architectural dimension to assist breeding, and (iii) interact with plant phenotyping for molecular breeding in embracing three-dimensional (3D) architectural traits. This study illustrates that FSPMs have great prospects in speeding up precision breeding for specific environments due to the capacity for guiding and integrating ideotypes, phenotyping, molecular design, and linking molecular basis to target phenotypes. Consequently, the promising great applications of FSPMs in crop science will, in turn, accelerate their evolution and vice versa.

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“…The software GroIMP contains also a powerful graph-drawing algorithm combining an energy-based layout with a tree layout [5]. Furthermore, XL was recently extended to support rewriting at several scale-levels simultaneously [12,13]. These were our main reasons for choosing the RGG approach and GroIMP for our purpose.…”

Section: Introductionmentioning

confidence: 99%

Multiscale Graph Grammars Can Generate Cayley Graphs of Groups and Monoids

Kurth

2020

Graph Transformation

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A graph grammar with parallel replacement of subgraphs, based on the single-pushout approach in graph rewriting, was designed which constructs Cayley graphs of monoids of transformations of a finite set, with permutation groups as a special case. As input, graph-based representations of a finite number of generating transformations have to be specified; they will then correspond to the edge types of the Cayley graph which is the final result of the rewriting process. The grammar has 7 + d rules, where d is the number of generators, and operates at two scale levels. The fine-scale level is the level of elements on which the transformations act and where their composition is calculated by parallel subgraph replacement. The coarse-scale level corresponds to the transformations themselves which are organized in the Cayley graph in a sequential rule application process. Both scale levels are represented in a single graph. The graph grammar was implemented in the programming language XL on the software platform GroIMP, a graph rewriting tool which was originally designed for simulating the growth of plants.

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An approach to multiscale modelling with graph grammars

Cited by 17 publications

References 41 publications

Reshaping Plant Biology: Qualitative and Quantitative Descriptors for Plant Morphology

Reshaping Plant Biology: Qualitative and Quantitative Descriptors for Plant Morphology

Functional–Structural Plant Models Mission in Advancing Crop Science: Opportunities and Prospects

Multiscale Graph Grammars Can Generate Cayley Graphs of Groups and Monoids

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