OpenAlea

An OpenSource platform for plant modeling

C. Pradal, S. Dufour-Kowalski,F. Boudon, C. Fournier, C. Godin

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MonolithicMonolithic SoftwareSoftware

InteroperableInteroperableSoftware Components Software Components for programmersfor programmers

InteroperableInteroperableSoftware Software Components Components for for modellersmodellers

Software Components Software Components for programmersfor programmers

time &

time &

complexity of b

iological pro

blems

complexity of b

iological pro

blems

http://www.scripps.edu/~sanner/

1.1. Construct the best model Construct the best model (efficient & simple) for (efficient & simple) for each new situationeach new situation

2.2. A general unified modelA general unified model

3.3. Defining common phenomenon Defining common phenomenon and concepts, and sharing and concepts, and sharing ‘elemental’ functionalities:‘elemental’ functionalities:

• Common to different situationsCommon to different situations

• ExtensibleExtensible

Modelling strategy

questionmodelquestion

platform

Biological Biological objectsobjects

MesureMesure

ModelingModeling

SimulationSimulation

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Plant modeling

ContextMulti-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 PrinciplesLanguage 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 ArchitectureD

ep

loym

en

t Tools

Component framework

ComponentPackage Manager Dataflow

Python Library

Existing ModelsC, C++, Fortran

math

GUI

shell

GUI

DatabaseXMLNumeric SciPy

f2py

Fortran Code

Boost, SWIG

C++ Classes, C Code

JEmbed

JavaClasses

Python

GUI

Vis

uale

a

PyQt4

Python as a Software Bus

(http://root.cern.ch)

mathmath

Very rich set of Python standard modules

GUI

shell

GUI

Several GUI toolkits

DatabaseXML

Very rich set of specialized generic modules

Numeric SciPy

Scientific modules

f2py

Fortran Code

Boost, SWIG

C++ Classes, C Code

JEmbed

JavaClasses

Gate

ways

to o

ther

fram

ew

ork

s

Component framework

Package Manager

Component

Python Interpreter

Dataflow

Widgets

ComponentSimple 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 togetherCollaborative development

– Gforge (subversion, forums, mailing lists)

– Wiki (User & developer documentation)

Software diffusion– Shared software repository

(14000 downloads)– Web site (100000 visits)

Coding & Modeling sprint– Pair programming– Development, bug fix, Use

cases, …

Already Integrated Packages

Plant architecture analysis - VPlants(Godin, Guedon et al)

Ecophysiological modelsBuissiere et al., 07

Fournier et al., 07

Sinoquet et al.

Meristem modeling(Stoma, Chopard et al.)

Conclusions

OpenAlea is an Open Source project– http://openalea.gforge.inria.fr

Promotes reusability– Interconnection of heterogeneous software

– Access to sub-models of applications

– Generic tools for software deployment

Improves accessibility– Visual programming

– Automatic widget creation