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International network of researchers working on
Plant Architecture Information Systems (PAIS)

Keywords: virtual plants, computational plant architecture, plant growth simulation

  1. Proposal summary

    The aim of this project is to foster international collaboration on plant architecture informatics. Plant Architecture Information Systems (PAIS) provide researchers in botany, forestry, horticulture, agronomy and ecology with common measurement methods, databases and tools. PAIS will facilitate studies on plant architecture and the use of this information for scientific and applied purposes. Especially, plant architecture information systems have a key-role to play in the building and assessment of plant growth models. This European-scale network is intended to take full advantage of the opportunities provided by the emerging field of research of "computational plant architecture".

  2. Scientific goals

    Plant architecture is a new paradigm in botany, forestry, agronomy and ecology. Traditional analysis methods describe plants using global variables. However, in the past two decades, an increasing number of studies in the different areas of plant science have used more detailed representations of plant structures. This resulted in creating a new area in plant science, focussed on the analysis and modelling of plant structures at various scales. Work in this new domain of "plant architecture" is expected to :

    • address new issues in forestry, horticulture and agronomy such as modelling plant plasticity, analysing the determinants of the interaction between growth and production, etc.
    • bring a gain in model accuracy.
    • favour the emergence of "robust models", (i.e. models that integrate plant structure representation in order to be easily adapted to different applications).
    • dramatically enhance the rendering of visual models.
    • enable modellers to integrate phenomena that occur at different space and time scale in their models. This is currently a crucial issue in plant architecture modelling.

    Yet, there is no consensus on a standard way to represent plant architecture. The current heterogeneity of representations and databases causes difficulties in defining generic methods and tools for both describing and measuring plant architectures. As a result, the research community currently lacks reusable databases and associated tools. However, botanical, mathematical and computer tools to deal with such representations are emerging. This suggests that a task of primary importance for the plant modelling community is to define i) common plant architecture data-bases, ii) translation schemes to exchange plant architecture data, iii) common data formats and tools to create standard plant architecture information systems that could be shared by research teams, with different modelling goals, throughout the world iv) training strategies to train young and senior researchers to these new techniques.

  3. Tasks of the network

    The aim of the network is not to redefine existing concepts and tools, but rather to take what is available (and sufficiently robust) and to extend it by new concepts and tools that have a global coherence at an international level. This means that every task in the project will mainly split into two stages: i) perform an inventory of existing resources (tools, data,...) ii) adapt and augment these resources to reach the network standard and goals.

    1. Definition of a standard plant architecture representation

      2. The heterogeneity of the representations used in the different domains of plant science makes it difficult to collect plant architecture information in a generic format to allow multiple uses. A major goal of the network will be to agree on a standard representation and corresponding encoding language, flexible enough to be adapted to various application requirements, and that everyone can use as a common language for representing plant architecture.

    2. Multi-purpose and reusable databases
      3.

      The current interest of the research community in plant structure/function models makes the collection of plant architecture data in the field an increasingly important issue. This can be used either :

      • to analyse different types of biological event distributions within plant architecture,
      • to define reference data for building plant structure/function models,
      • to define initial data for simulations of plant growth,
      • or to assess model output compared with actual data.

      However, collecting architecture data requires the definition of complex experimental and observation protocols and is often time-consuming. The aim of this task is thus to create plant architecture databases of different plant species in different application domains using standard formats. Such standard databases can be created either from existing data or from new data collected in the field during the project life using PAIS standard format and tools. A library of these standard databases would be available on the web.

    3. Tools for analysing plant architecture databases
      4.

      Different types of tools to explore and analyse plant architecture are already available from partners or need to be developed (e.g. to automate plant architecture measurement and digitising, to access to and extract data from plant architecture, etc.). In order to have a consistent and efficient use of these tools, they must be integrated within a common software platform, providing the user a high degree of interactivity with plant architecture databases. AMAPmod - a free software for analysing plant architecture developed at Cirad - is an example of such a platform. This software could be used within the project as a core element to develop further tools.

    4. Developing standard interchange protocols
      5.

      A crucial need for the scientific community is to exchange plant architecture data. This can be to explain a method, to compare models, to allow other teams to reuse data, etc. For this to be possible, standard interchange protocols must be defined to translate data from one coding language into the other.

    5. Assessment of plant growth models
      6.

      The availability of common databases in plant science would enable modellers to assess their models based on common and publicly available data. Such shared databases have already been developed in other scientific domains: in medical science with the "visible man project", in language processing where the collection of "person-machine corpora" is frequently carried out by several teams to share the expenses of such task, in image processing where standard images are frequently used to assess the performance of a new algorithm, etc. This task is intended to show the interest of reusable of databases in the context of plant architecture modelling by allowing discussion between different modelling approaches based on common databases.

    6. Training strategy
      7.

      The definition of plant architecture information systems and corresponding methodology will be successful only if a simultaneous training programme is defined so that researchers can learn how to use these tools. A special effort must be devoted within the network to the training of young researchers since they will naturally use, develop and promote the method in their future research activity. This training will be carried out in three directions:

      • First, courses can be made to form students and researchers to these new techniques. In France for instance, training sessions (in French) on AMAPmod (a program for analysing plant architecture data) and digitising tools have been organised since 1998 and are held twice a year during one week ("écoles-chercheur Cirad/Inra"). The network will provide us the opportunity to create corresponding English sessions, opened to people from the network.
      • Second, once a year, we plan to organise a workshop (each time organised by a different partner) on different items (e.g. plant architecture digitising, analysis of root systems, software tools for analysing plant architecture, assessment of structure-function models).
      • Third, the young researchers will be thoroughly integrated in the research activities of the respective teams.