OpenAlea An OpenSource platform for plant modeling C. Pradal, S. Dufour-Kowalski, F. Boudon, C. Fournier, C. Godin

Monolithic Software Interoperable Software Components for programmers InteroperableSoftwareComponents for modellers Software Components for programmers time & complexity of biological problems

1.Construct the best model (efficient & simple) for each new situation 2.A general unified model 3.Defining common phenomenon and concepts, and sharing ‘elemental’ functionalities: Common to different situationsCommon to different situations ExtensibleExtensible Modelling strategy question model question platform

Biological objects Mesure Modeling Simulation X X X X X X U1 I12 I13 U2 F1 U2 I2 I1 I8 I9 I6 I10 I11 F1 U1 U2 I10 I15 X X X X U2 I7 I8 I9 I10 X F1 U2 I1 S1 F1 U1 U2 F1 U2 U1 U2 F1 U < + < < < < U1 U2 F1 S1 F1 + U2 < A91 A92 A91 A92 A91 A92 < + < < F1 leaves roots f r Plant modeling

Context Multi-disciplinary domain –It involves a variety of disciplines and expertise. Low reusability –Combining or Reusing existing software is complex Different OS, different programming languages No common standards or data-structures Building models is expensive –Development –Validation –Distribution, Documentation, Training

OpenAlea Goals Promoting share within a community –Reuse software & tools –Share development between various teams –Share databases & training effort With a common software platform –Integration of existing models & tools –Rapid development of new applications –Enhance accessibility (GUI) –Quality rules

Design Principles Language centric –Common modeling language –Glue language Component architecture –Dynamic composition –High-level dataflow approach Visual programming –Graphical model representation –Automatic GUI generation Shared deployment tools –Build, packaging, distribution, installation, upgrade Multi-platform (Linux, Windows)

OpenAlea Architecture Deployment Tools Component framework Component Package Manager Dataflow Python Library Existing Models C, C++, Fortran math GUI shell GUI DatabaseXMLNumericSciPy f2py Fortran Code Boost, SWIG C++ Classes, C Code JEmbed Java Classes Python GUI Visualea PyQt4

Python as a Software Bus ( math Very rich set of Python standard modules GUI shell GUI Several GUI toolkits DatabaseXML Very rich set of specialized generic modules NumericSciPy Scientific modules f2py Fortran Code Boost, SWIG C++ Classes, C Code JEmbed Java Classes Gateways to other frameworks

Component framework Package Manager Component Python Interpreter Dataflow Widgets

Component Simple Python function –Multiple Input and Output arguments (ports) –Typed interface –Documentation def linearmodel(x=0, a=0., b=0): “ return ax+b ” return a*x+b Port name : ‘a’ Interface : IFloat

Dataflow Graphical model Visual representation of a model Connect components in a directed graph Data flow through edges Model of computation Functional (deterministic) Lazy evaluation

Macro component

Functions and loops

Deployment Tools OpenAlea.Installer –Search, download and install dependencies from the web –List available packages found on a central repository (OpenAlea website) SConsX –Simplify the build of complex packages (C, C++, Fortran)

Working together Collaborative development –Gforge (subversion, forums, mailing lists) –Wiki (User & developer documentation) Software diffusion –Shared software repository (14000 downloads) –Web site ( visits) Coding & Modeling sprint –Pair programming –Development, bug fix, Use cases, …

Already Integrated Packages Plant architecture analysis - VPlants (Godin, Guedon et al) Ecophysiological models Buissiere et al., 07 Fournier et al., 07 Sinoquet et al. Meristem modeling (Stoma, Chopard et al.)

Conclusions OpenAlea is an Open Source project – Promotes reusability –Interconnection of heterogeneous software –Access to sub-models of applications –Generic tools for software deployment Improves accessibility –Visual programming –Automatic widget creation