title: A rule-based model of barley morphogenesis, with special respect to shading and gibberellic acid signal transduction.
abstract: OBJECTIVE
  Functional-structural plant models (FSPM) constitute a paradigm in plant modelling that combines 3D structural and graphical modelling with the simulation of plant processes. While structural aspects of plant development could so far be represented using rule-based formalisms such as Lindenmayer systems, process models were traditionally written using a procedural code. The faithful representation of structures interacting with functions across scales, however, requires a new modelling formalism. Therefore relational growth grammars (RGG) were developed on the basis of Lindenmayer systems.
  
  
  METHODS
  In order to implement and test RGG, a new modelling language, the eXtended L-system language (XL) was created. Models using XL are interpreted by the interactive, Java-based modelling platform GroIMP. Three models, a semi-quantitative gibberellic acid (GA) signal transduction model, and a phytochrome-based shade detection and object avoidance model, both coupled to an existing morphogenetic structural model of barley (Hordeum vulgare L.), serve as examples to demonstrate the versatility and suitability of RGG and XL to represent the interaction of diverse biological processes across hierarchical scales.
  
  
  RESULTS
  The dynamics of the concentrations in the signal transduction network could be modelled qualitatively and the phenotypes of GA-response mutants faithfully reproduced. The light model used here was simple to use yet effective enough to carry out local measurement of red:far-red ratios. Suppression of tillering at low red:far-red ratios could be simulated.
  
  
  CONCLUSIONS
  The RGG formalism is suitable for implementation of multi-scaled FSPM of plants interacting with their environment via hormonal control. However, their ensuing complexity requires careful design. On the positive side, such an FSPM displays knowledge gaps better thereby guiding future experimental design.
authors.affiliation: Crop and Weed Ecology Group, Wageningen UR, Haarweg 333, 6709 RZ Wageningen, The Netherlands. gerhard.buck-sorlin@wur.nl
authors.forename: Gerhard
authors.initials: G
authors.lastname: Buck-Sorlin
authors.forename: Reinhard
authors.initials: R
authors.lastname: Hemmerling
authors.forename: Ole
authors.initials: O
authors.lastname: Kniemeyer
authors.forename: Benno
authors.initials: B
authors.lastname: Burema
authors.forename: Winfried
authors.initials: W
authors.lastname: Kurth
mesh_terms: D000465:Algorithms; D003198:Computer Simulation; D005875:Gibberellins / Q000378:metabolism / Q000494:pharmacology*; D001467:Hordeum / Q000254:growth & development* / Q000378:metabolism; D008962:Models, Theoretical; D009024:Morphogenesis / Q000187:drug effects*; D010937:Plant Growth Regulators / Q000378:metabolism / Q000494:pharmacology; D015398:Signal Transduction; D012984:Software
chemical_list: D005875:Gibberellins; D010937:Plant Growth Regulators; C007842:gibberellic acid