Journées INRA - INRIA
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Transcript of Journées INRA - INRIA
Les sciences de la vie et de
l'environnement
dans la stratégie de l'INRIA
Journées INRA - INRIA
Mai 2007
Journées INRA - INRIA 2
Les sciences de la vie et de l'environnement dans la stratégie de l'INRIA
Introduction
Quelques illustrations
Principales thématiques de recherche
Plan stratégique 2008 - 2012
Journées INRA - INRIA 3
INRIA
Research in Computer and Information Science and Engineering INRIA fosters a close integration of
research - development - transfer
It offers to associated universities and research partners Scientific and organizational leadership in its areas A vision, a strategic plan, and a research road-map Research facilities and support Strong industrial partnership for technology development &
transfer
Journées INRA - INRIA 4
INRIA
A total work force of 3600 persons 1100 researchers and faculty members 1000 doctoral candidates 1000 engineers, technicians and staff 500 post-docs and visiting scientists
2100 INRIA employees including 500 permanent scientists1500 partners employees
INRIA budget of 165 M€ Over 20% from grants and IP products Consolidated budget of INRIA activities : 250 M€
Journées INRA - INRIA 5
Research centers
LORIANancy
INRIA Rhône-AlpesGrenoble
INRIASophia Antipolis
IRISARennes
INRIA FUTURSBordeaux
Metz
INRIA FUTURS, Lille
Lannion
Marseille
Lyon
Montpellier
INRIA FUTURS Saclay
Nantes
Besançon
Strasbourg
INRIARocquencourt
Paris
Journées INRA - INRIA 6
Nancy
Grenoble
Rennes
Sophia Antipolis
Paris-Rocquencourt
Research Centers
Lille
Saclay
Bordeaux
Journées INRA - INRIA 7
Environment and life sciences at INRIA
Over 20 project-teams directly involved in this domains
Helix, Symbiose, Contraintes, Bang, ABS , Vista
Digiplants, Comore, VirtualPlants
Clime, Moïse, Mere, Bang, Ariana
Asclepios, Demar, Odyssee, Sysiphe, Visages, Reo
About as many groups contribute to the domain Apics, Coprin, Evasion, Anubis, Geometrica, Caiman, Opale, Orion, Smash, Omega, Tropics, Imedia, Dream Orpailleur, Cortex, Tao, Texmex, etc.
Journées INRA - INRIA 8
Les sciences de la vie et de l'environnement dans la stratégie de l'INRIA
Introduction
Quelques illustrations
Principales thématiques de recherche
Plan stratégique 2008 - 2012
Journées INRA - INRIA 9
MOISE : Modélisation, Observations, Identification en Sciences de l’Environnement
Mathematics and calculus for the direct and inverse modeling in direct geophysicsDesign and optimization of complexe systems complexes (several coupled models, data assimilation)Processing of heterogeneous informationUncertainty quantification
Understanding and predicting natural processes : meteorology, oceanography, hydrology, glaciology Social challenges: water resources, risk prevention and management, evolution of the climate, territory planning,
Journées INRA - INRIA 10
Visages :Vision, Action et informations de santéJoint team INRIA-INSERM (U746)
Neuroimaging and modeling
Multimodal sensors and
churgical actuators
E-science: biomarkers,
mining, certification in
pharmacology
Journées INRA - INRIA 11
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Efficience de l’eau
Biomasse Photosynthèse
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Journées INRA - INRIA 12
Helix : Understanding Bacterial Stress Responses Bacteria have capacity to adapt to variety of environmental
stresses (lack of nutrients, heat shock, crowding) Bacterial stress responses are controlled by complex network of
molecular interactions A model of E. coli carbon starvation network using piecewise-
affine models of gene regulation has been designed Experimental verification by means of real-time measurements of
gene expression shows the quality of model prediction
Escherichia coli Carbon starvation network Gene expression measurements
Journées INRA - INRIA 13
Contraintes : cell and cyrcadien cycles
Biochemical model: Transition system (with continuous time) Biological property: Temporal Logic formula Biological validation: Model-checking
Models of cell cycle: over 800 reactions, 165 genes and proteinsParteners: Institut Curie and FP6 projects
Model
Boolean
Differential
Stochatisc
Temporal
BIOCHAM
Simulation
Query evaluation
Reaction rule learning
Parameter search
Biological properties
Temporal logic
Constraints
Journées INRA - INRIA 14
Les sciences de la vie et de l'environnement dans la stratégie de l'INRIA
Introduction
Quelques illustrations
Principales thématiques de recherche
Plan stratégique 2008 - 2012
Journées INRA - INRIA 15
Biomedical Imaging
Constant stream of better imaging & signal modalities
Provide complementary anatomical & functional info with ever increasing spatial & temporal resolution
From molecular to cellular to organ scales
Emerging new modalities and therapies
Emerging Large Databases
200 microns
Neuro-muscular junctionsMicrovessels & leukocytes
Bladder cells
Brain
Heart
Journées INRA - INRIA 16
Privileged Role of in vivo Biomedical Imaging
Visualize, analyze and quantify physiological processes and pathological modifications in living systems
Analyze and quantify genesis processes : organs, tumors, vessels, plasticity, etc.
Mark cellular populations and track their migration, phenotypic modifications, differentiation, apoptosis, etc.
Observe biological processes of synthesis, expression, translation, apoptosis, etc.
Journées INRA - INRIA 17
Virtual Physiological Human Organs
Build personalized virtual models of human physiological systems (e.g. cardiac, respiratory, digestive, nervous central and peripheral, reproductive, etc.) which can be used for
quantitative diagnosis,
prevention of diseases,
therapy planning and simulation
Journées INRA - INRIA 18
Virtual Neuronal Networks
Simulate feedforward and backward dynamically connected sets of very large populations of spiking neurons to emulate significant aspects of visual perception.
Explore the use of the processing of the signals generated by brain electrical sources to design new interactions between humans and their artifacts.
Journées INRA - INRIA 19
Large models of Cells, Plants & Ecosystems Build, simulate, analyze and optimize such large models to
explain the emergence of global properties from microscopic interactions.
Journées INRA - INRIA 20
Computational Structural Biology
Investigate the relationship between the structure of macro-molecules (DNA, RNA, Proteins) and their function.
Journées INRA - INRIA 21
Computational Physiology
Reproduce Functional properties of living systems at various scales molecules, proteins, cells
cells, tissues, organs, systems, body, etc.
Personalization requires to choose the right level of complexity (observations) and a limited number of parameters
Model normal physiology and physiopathologyINRIA in silico electro-
mechanical cardiac model
nano
micro
meso
macro
ATP
sarcomeres
fibers
organ
Journées INRA - INRIA 22
Computational Anatomy
Statistics on Anatom
Build standard computational models
Establish plausible variations around standards
Constrain Model Personalization
Detect abnormal Deviations
Journées INRA - INRIA 23
Biomedical Image and Signal Analysis
New tools to extract and fuse pertinent information from complex multimodal, multidimensional and multiscale signals
segmentation, registration, tracking, deformation, etc.
mining, indexing, learning, etc.
across time, modalities, scales, individuals, populations… Design multi-layered advanced image processing algorithms
Geometrical,
Statistical
Physical,
Physiological
Journées INRA - INRIA 24
Data Assimilation Techniques
Innovative methods to solve very large inverse problems
Identification of large number of parameters from huge quantity of measurements
Iterative vs. variational methods
Time constraints
Journées INRA - INRIA 25
Scientific Computing
Importance of scientific computing for direct simulationLarge scale/dimension problemsMultiscale/heterogeneous problemsUncertainties modelingRobustness of optimization
Computational GeometryComputational PhysicsComputational ChemistryComputational Molecular BiologyComputational Structural Biology
Journées INRA - INRIA 26
Exploring Biological Information
Collect, structure huge amounts of biological information
Add semantics
Represent and Analyze Large Biological Networks
Model their dynamics
Journées INRA - INRIA 27
Exploit massively parallel computing
Very large data
Heterogeneous data
Distributed data
Confidentiality constraints
Time constraints
Grid computing
Parallel computing
Semantics grids
technologies
Semantic web
Dedicated computing
platforms
Journées INRA - INRIA 28
Les sciences de la vie et de l'environnement dans la stratégie de l'INRIA
Introduction
Quelques illustrations
Principales thématiques de recherche
Plan stratégique 2008 - 2012
Journées INRA - INRIA 29
INRIA Strategic Plan for 2008 - 2012
Research Areas
Algorithmic of Biology & Medicine
Ubiquitous Information, Computation & Communication
Interacting with Real & Virtual Worlds
Modeling, Simulating, & Optimizing Complex Systems
Guarantied & Secure Computing
Computational Sciences
Computational Engineering : Embedded Systems
Journées INRA - INRIA 30
Algorithmic of Biology and Medicine
Design and develop computational models of living systems
matching biomedical images/signals/measurements
to better understand the living systems under study
to better predict their natural normal or pathological evolution
to better plan and simulate the potential effects of an
interaction
to better control them and repair their possible dysfunctions
Journées INRA - INRIA 31
Algorithmic of Biology and Medicine
Computational Models
of human body
Medical Images
and Signals
Interpretation(diagnosis)
Identification(personalization)
Prediction ofevolution
Therapysimulation
Therapy planning
GeometryStatisticsPhysics
Physiology
Journées INRA - INRIA 32
Algorithmic of Biology and Medicine
Computational Physiology : reproduce personalized functional
properties of living systems at various scales
Computational Anatomy: standard and abnormal models
Biomedical Image and Signal Analysis
Data Assimilation Techniques: very large inverse problems
Scientific Computing : computational geometry, physics,
chemistry, molecular biology, structural biology
Exploring biological Information
Exploiting massively parallel computing
Journées INRA - INRIA 33
Numerical Sciences
Digital cells
Digital plants
Digital ecology
Digital biosphere and environment
Digital material
Journées INRA - INRIA 34
Digital Cell
Computational structural biology Relationship between structure and action of complex
molecular machinery Functional genomic, genes - protein expression and regulation
networks Assembly and mechanical functions of the cytoskeleton in the
cell motility and dynamic behavior
Journées INRA - INRIA 35
Digital ecology
Heterogeneous representation, modeling and integration
Differential models for low trophic levels
Structured population models
Individual-based models for higher trophic species
taking into account the geophysical environment, biotope, interaction between species, etc.
Integration of data from sensor networks, satellites and geo-referenced images
Prediction, visualization, conservation planning
Journées INRA - INRIA 36
Platforms and systems for
Monitoring, forecasting, risk management at local and global scales
Integrating models and data
Measured evolution of the biosphere
To assess the landscape modifications on earth, the diffusion of
a pollutant in a river, the plankton composition in the oceans
To predict the future evolution of the biotope
Digital Environment
Journées INRA - INRIA 37
Direct modeling: mathematical and numerical methods, scientific
computing, probabilistic modeling
Forecasting error assessment: modeling uncertainty by
deterministic or stochastic methods, forecasting of extreme events
Inverse modeling: data assimilation, optimal control, filtering
Sensor networks
Large-scale issues
Digital Environment
Journées INRA - INRIA 38
Automatic image indexing, retrieval and analysis Data representation and processing: sensors fusion, Geographic
Information Systems, decision support systems, etc. 3D visualization: visualization of forecast results, use of virtual
environments for what-if scenario, CAD Software engineering: management of complex and evolving
systems Grid computing: access to distributed computing and data
resources, parallel computing, real-time and security issues
Digital Environment