Section: New Software and Platforms

Platforms

Platform OpenAlea

OpenAlea is an open-software platform for interdisciplinary research in plant modeling and simulation. This scientific workflow platform is used for the integration and comparison of different models and tools provided by the research community. It is based on the Python (http://www.python.org) language that aims at being both a glue language for the different modules and an efficient modeling language for developing new models and tools. OpenAlea currently includes modules for plant simulation, analysis and modeling at different scales (V-Plants modules), for modeling ecophysiological processes (Alinea modules) such as radiative transfer, transpiration and photosynthesis (RATP, Caribu, Adel, TopVine, Ecomeristem) and for 3D visualization of plant architecture at different scales (PlantGL).

OpenAlea is the result of a collaborative effort associating 20 french research teams in plant modeling from Inria, CIRAD, INRA and ENS Lyon. The Virtual Plants team coordinates both development and modeling consortia, and is more particularly in charge of the development of the kernel and of some of the main data structures such as multi-scale tree graphs and statistical sequences.

OpenAlea is a fundamental tool to share models and methods in interdisciplinary research (comprising botany, ecophysiology, forestry, agronomy, applied mathematics and computer science approaches). Embedded in Python and its scientific libraries, the platform may be used as a flexible and useful toolbox by biologists and modelers for various purposes (research, teaching, rapid model prototyping, communication, etc.).

New methodological developments around scientific workflows in OpenAlea have been done recently.

Platform Sofa

Our team is increasingly using the platform SOFA developed at Inria by other teams, in conjunction with OpenAlea, to model biomechanics of plant tissues. SOFA (https://www.sofa-framework.org) is an Open Source framework primarily targeted at real-time simulation, with an emphasis on biological simulation. It is mostly intended for the research community to help develop new algorithms, but can also be used as an efficient prototyping tool. Based on an advanced software architecture, it allows the creation of complex and evolving simulations by combining new algorithms with algorithms already included in SOFA, the modification of most parameters of the simulation (deformable behavior, surface representation, solver, constraints, collision algorithm, etc. ) by simply editing an XML file, the building of complex models from simpler ones using a scene-graph description, the efficient simulation of the dynamics of interacting objects using abstract equation solvers, the reuse and easy comparison of a variety of available methods. It has been extensively used by our team in the recent years to conduct virtual mechanical experiments on plant tissues (see section 6.2.3).