openalea an opensource platform for plant modeling c. pradal, s. dufour-kowalski, f. boudon, c....
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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
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complexity of b
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http://www.scripps.edu/~sanner/
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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
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Biological Biological objectsobjects
MesureMesure
ModelingModeling
SimulationSimulation
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Plant modeling
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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
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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
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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)
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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
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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
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Component framework
Package Manager
Component
Python Interpreter
Dataflow
Widgets
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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
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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
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Macro component
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Functions and loops
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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)
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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, …
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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.)
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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