Theme DEVMP - Generic software for plant modeling

Scientific objective

To develop federative research software to respond efficiently to scientists’ requests for plant modeling by exploring approaches focusing on genericity, mutualization and integration.
In particular to (i) simulate the growth and dynamics of agronomic and forestry systems, (ii) facilitate the measurement and simulation of plant 3D architecture, (iii) explore and describe the structure of one or several individuals, from a single small plant to a group of adult trees, (iv) enable interoperability with other softwares or platforms through standard import/export formats or (v) simulate biophysical processes.

Approach

Genericity would enable new projects to start more rapidly through the use of frameworks designed for reuse (e.g. the generic Capsis framework). The aim of integration is capitalizing on investments in long-term modeling software, software suites or platforms in which available tools form an increasingly larger corpus, to be shared with new partners in a win-win perspective.
The widest accessibility is guaranteed by a system of distribution licenses (generally free software licenses) and specific charters that clearly explain the rights and responsibilities of all the partners. Specific details are included to allow maximum sharing while respecting everyone's intellectual property rights.
The generic developments are mainly conducted in the framework of three long-term projects:

  •  Capsis: a software platform for forestry dynamics models,
  •  AMAPstudio: a software suite for modeling plant 3D architecture,
  •  Greenlab GL5: a software suite that implements the Greenlab model.

This research is dedicated to building software not building models.

Expected results

Several levels of service for plant modelers:

  •  Simple access to the usual features (loading, simulating, viewing, exploring, editing, exporting, etc.) with interactive software;
  •  Helping researchers incorporate their models in simulators: after investing time in a short programming course, scientists can benefit from a customized assisted start up and long-term support for their project;
  •  Help defining the specifications of new tools that address a collective need (data input, analysis, graphical outputs, etc.), which are then written and maintained by developers;
  •  Provision of software bricks that are interoperable with other software environments.

These research softwares can be (i) used in high visibility projects, (ii) a technical base for partnerships between scientists and (iii) knowledge transfer vectors to the downstream partners of the member scientists.

Scientific projects

Acronym Title Duration/th>
STEM-LEAFSTudies based on Experimental and Modelled wavefor for the LEAF (Lidar for Earth And Forests) mission2013 - 2016
MOCAF 2 - PRINCIPESModélisation de la Croissance, de l'Architecture et de la Floraison2012 - 2014
GUYAFORUn réseau de dispositifs permanents pour un suivi à long terme des écosystèmes forestiers guyanais 2007-2010 : Estimation du stockage de carbone des forêts guyanaises2009 - 2010

Majpr publications

All publications
  • Griffon S., de Coligny F., 2014. AMAPstudio: an Editing and Simulation Software Suite for Plants Architecture Modelling. Ecological Modelling, 290:3-10. [Editor link]
  • Dufour-Kowalski S., Courbaud B., Dreyfus P., Meredieu C., de Coligny F., 2012. Capsis: an open software framework and community for forest growth modelling. Annals of Forest Science, 69:221–233. [Editor link]
  • de Reffye, P., Kang, M. Z., Hua, J., Auclair, D., 2012. Stochastic modelling of tree annual shoot dynamics. Annals of Forest Science, 69 (2) : 153-165. [Editor link]

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