title: AmapSim: a structural whole-plant simulator based on botanical knowledge and designed to host external functional models.
abstract: OBJECTIVE
  AmapSim is a tool that implements a structural plant growth model based on a botanical theory and simulates plant morphogenesis to produce accurate, complex and detailed plant architectures. This software is the result of more than a decade of research and development devoted to plant architecture. New advances in the software development have yielded plug-in external functions that open up the simulator to functional processes.
  
  
  METHODS
  The simulation of plant topology is based on the growth of a set of virtual buds whose activity is modelled using stochastic processes. The geometry of the resulting axes is modelled by simple descriptive functions. The potential growth of each bud is represented by means of a numerical value called physiological age, which controls the value for each parameter in the model. The set of possible values for physiological ages is called the reference axis. In order to mimic morphological and architectural metamorphosis, the value allocated for the physiological age of buds evolves along this reference axis according to an oriented finite state automaton whose occupation and transition law follows a semi-Markovian function.
  
  
  RESULTS
  Simulations were performed on tomato plants to demonstrate how the AmapSim simulator can interface external modules, e.g. a GREENLAB growth model and a radiosity model.
  
  
  CONCLUSIONS
  The algorithmic ability provided by AmapSim, e.g. the reference axis, enables unified control to be exercised over plant development parameter values, depending on the biological process target: how to affect the local pertinent process, i.e. the pertinent parameter(s), while keeping the rest unchanged. This opening up to external functions also offers a broadened field of applications and thus allows feedback between plant growth and the physical environment.
authors.affiliation: CIRAD, Cirad-Cnrs-Inra-Ird-Université Montpellier, France. barczi@cirad.fr
authors.forename: Jean-François
authors.initials: JF
authors.lastname: Barczi
authors.forename: Hervé
authors.initials: H
authors.lastname: Rey
authors.forename: Yves
authors.initials: Y
authors.lastname: Caraglio
authors.forename: Philippe
authors.initials: P
authors.lastname: de Reffye
authors.forename: Daniel
authors.initials: D
authors.lastname: Barthélémy
authors.forename: Qiao Xue
authors.initials: QX
authors.lastname: Dong
authors.forename: Thierry
authors.initials: T
authors.lastname: Fourcaud
mesh_terms: D003198:Computer Simulation; D063245:Plant Development; D018521:Plant Physiological Phenomena; D010944:Plants / Q000033:anatomy & histology; D012984:Software; D013997:Time Factors