OpenAlea : Open Source
software to model plant growth
Christophe Pradal
Inria project team VirtualPlants
CIRAD/INRA UMR AGAP
8th Meeting of the European TTO Circle
19 June 2015
3 French Research Institutes
• Information and Communication Science and Technologies (Inria)
• Food, Agriculture and Environment (Cirad & INRA)
Informatics &
Mathematics
8
Research Centers
in France
Agricultural Research
for Development
12
Regional offices in France,
overseas & worldwide
Agricultural Research
Food, Agriculture, Environment
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Research Centers
in France
Scientific institutions under the authority of the Ministry of
Research, the Ministry of Industry and the Ministry of Agriculture
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Plant modelling
Different
scales
Data
acquisition
Modeling
Simulation
3
OpenAlea Objectives
Share knowledge
•
•
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Reuse software & tools
Share development between various team
Exchange experience & data
Share training effort
Component based software architecture
• Integration of existing software & tools
• Rapid development of new models
• Quality rules
4
OpenAlea design principles
Language centric
– Common modelling language
– Glue language
– 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, Mac OS X
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Component architecture
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OpenAlea
OpenAlea (Pradal et al, 08)
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•
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Plant modelling
Tissue modelling
Scientific Workflow
6
OpenAlea community
Designers
• Software Platform Development
• Counsel, training and assistance to Modellers
Modellers
• Development and Integration of models and tools
• Validation of existing models
• Users counsel, training and assistance
Users
• Share experimental data
• Define scenario
• Provide feedback
Structure of the community :
3 interacting groups with different needs and interests
7
Open Source Scientific Community
Free Software License (IPR Management)
• OpenAlea : CeCILL-C (aka L-GPL)
• Components / Models :
 Both Open or Close source license
Software Release
• Only Open Source components are released
• Systematic Peer Review
• Quality Assurance Rules
 Test, Code Quality, Documentation
Collaborative Development
• Shared development between various teams
 Inria gforge, GitHub
• Shared Methodology and Best Practices
 Inside OpenAlea and with other Open Source projects
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Free Software -
Scientific advantages
Scientific Validation
• Access to the source code: Verification of models and algorithms
• Reproduce scientific experiment on different data sets
Scientific collaboration
• Published models are directly available
• Improvement and Enhancement of existing models by different teams
Project Sustainability
• When a project stop, any team can continue its development
Intellectual Property protection
• Free Software license define explicit rules both for authors and users.
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Agile Project Management
Animation of the community: Let’s sprint
Sprint
• Appear in Open Source conference (1st Hackathon OpenBSD 1999)
• Pair programming and Test Driven Development
Coding Sprint
• Mathematicians & Computer Scientists
• Duration : 3 days, From 10 to 20 developpers
• One cycle = One task = ½ day
Modelling Sprint
• Biologists and Computer Scientists
• Model integration and informal training
• Foster collaborations
10
Governance & Strategy
OpenAlea Scientific Board
• Software Review as an editorial committee
• Animation & Training
• Inria, Cirad, INRA, universities and industry (Arvalis)
OpenAlea Charter
• Principles, Rights and Duties
Funding
• Research Institutes, Fundations (Agropolis)
• National & European projects
Some facts
• 580.000 downloads, 20 active developers, 90 models
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Industry involvement in R&D
Scientific collaboration between academic and industry
• Industry fund research projects
Industry involvement in multi-disciplinary projects
• Provide large field experiment data and “know-how”
• Benefit of multi-disciplinary network and state-of-the art models
New Technological projects (Phenomics, Precision agriculture)
• Provide & use new technology (e.g. sensors, software pipelines)
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Transfer to the Plant modelling community
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Epidemiology on Plant Architecture
Multidomain
FSPM
Adel-Septo
Echap Project
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Plant Phenomics, Breeding, and Big Data
• Monitoring of plants by Imaging
• High-throughput (1650 plants/day
during 3 weeks)
• Genotype / Phenotype /
Environment
• Grid Computing with OpenAlea
120 images/plant 5 To / week
Phenoarch (INRA, Lepse)
CSIRO Plant Phenomics
Phenome project
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Questions?
16