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Les sciences de la vie et de l'environnement dans la stratégie de l'INRIA Journées INRA - INRIA Mai 2007.

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Presentation on theme: "Les sciences de la vie et de l'environnement dans la stratégie de l'INRIA Journées INRA - INRIA Mai 2007."— Presentation transcript:

1 Les sciences de la vie et de l'environnement dans la stratégie de l'INRIA Journées INRA - INRIA Mai 2007

2 Journées INRA - INRIA2 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

3 Journées INRA - INRIA3 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

4 Journées INRA - INRIA4 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 scientists 1500 partners employees INRIA budget of 165 M Over 20% from grants and IP products Consolidated budget of INRIA activities : 250 M

5 Journées INRA - INRIA5 Research centers LORIA Nancy INRIA Rhône-Alpes Grenoble INRIA Sophia Antipolis IRISA Rennes INRIA FUTURS Bordeaux Metz INRIA FUTURS, Lille Lannion Marseille Lyon Montpellier INRIA FUTURS Saclay Nantes Besançon Strasbourg INRIA Rocquencourt Paris

6 Journées INRA - INRIA6 Nancy Grenoble Rennes Sophia Antipolis Paris-Rocquencourt Research Centers Lille Saclay Bordeaux

7 Journées INRA - INRIA7 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.

8 Journées INRA - INRIA8 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

9 Journées INRA - INRIA9 MOISE : Modélisation, Observations, Identification en Sciences de lEnvironnement Mathematics and calculus for the direct and inverse modeling in direct geophysics Design and optimization of complexe systems complexes (several coupled models, data assimilation) Processing of heterogeneous information Uncertainty quantification Understanding and predicting natural processes : meteorology, oceanography, hydrology, glaciology Social challenges: water resources, risk prevention and management, evolution of the climate, territory planning,

10 Journées INRA - INRIA10 Visages :Vision, Action et informations de santé Joint team INRIA-INSERM (U746) Neuroimaging and modeling Multimodal sensors and churgical actuators E-science: biomarkers, mining, certification in pharmacology

11 Journées INRA - INRIA11 No stress W. stress Efficience de leau Biomasse Photosynthèse Organogénèse Fonction puits Digiplante : GreenLab3

12 Journées INRA - INRIA12 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 networkGene expression measurements

13 Journées INRA - INRIA13 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 proteins Parteners: Institut Curie and FP6 projects Model Boolean Differential Stochatisc Temporal BIOCHAM Simulation Query evaluation Reaction rule learning Parameter search Biological properties Temporal logic Constraints

14 Journées INRA - INRIA14 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

15 Journées INRA - INRIA15 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 junctions Microvessels & leukocytes Bladder cells Brain Heart

16 Journées INRA - INRIA16 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.

17 Journées INRA - INRIA17 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

18 Journées INRA - INRIA18 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.

19 Journées INRA - INRIA19 Large models of Cells, Plants & Ecosystems Build, simulate, analyze and optimize such large models to explain the emergence of global properties from microscopic interactions.

20 Journées INRA - INRIA20 Computational Structural Biology Investigate the relationship between the structure of macro- molecules (DNA, RNA, Proteins) and their function.

21 Journées INRA - INRIA21 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 physiopathology INRIA in silico electro- mechanical cardiac model nano micro meso macro ATP sarcomeres fibers organ

22 Journées INRA - INRIA22 Computational Anatomy Statistics on Anatom Build standard computational models Establish plausible variations around standards Constrain Model Personalization Detect abnormal Deviations

23 Journées INRA - INRIA23 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

24 Journées INRA - INRIA24 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

25 Journées INRA - INRIA25 Scientific Computing Importance of scientific computing for direct simulation Large scale/dimension problems Multiscale/heterogeneous problems Uncertainties modeling Robustness of optimization Computational Geometry Computational Physics Computational Chemistry Computational Molecular Biology Computational Structural Biology

26 Journées INRA - INRIA26 Exploring Biological Information Collect, structure huge amounts of biological information Add semantics Represent and Analyze Large Biological Networks Model their dynamics

27 Journées INRA - INRIA27 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

28 Journées INRA - INRIA28 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

29 Journées INRA - INRIA29 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

30 Journées INRA - INRIA30 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

31 Journées INRA - INRIA31 Algorithmic of Biology and Medicine Computational Models of human body Medical Images and Signals Interpretation (diagnosis) Identification (personalization) Prediction of evolution Therapy simulation Therapy planning Geometry Statistics Physics Physiology

32 Journées INRA - INRIA32 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

33 Journées INRA - INRIA33 Numerical Sciences Digital cells Digital plants Digital ecology Digital biosphere and environment Digital material

34 Journées INRA - INRIA34 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

35 Journées INRA - INRIA35 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

36 Journées INRA - INRIA36 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

37 Journées INRA - INRIA37 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

38 Journées INRA - INRIA38 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

39 Journées INRA - INRIA39 Inria Strategic Plan Digital Sciences Digital engineering Algorithmic of Biology & Medicine Information, Computation & Communication Everywhere Interacting with Real & Virtual Worlds Modeling, Simulating, & Optimizing Complex Systems Guarantied & Secure Computing

40 Journées INRA - INRIA40 Axes du plan 2003-2007 Infrastructures des réseaux et des services de communication Informations et données multimédia Fiabilité et la sécurité des systèmes à logiciel prépondérant Coupler modèles et données pour simuler et contrôler les systèmes complexes Combiner simulation, visualisation et interaction Modéliser le vivant Intégrer pleinement les STIC dans les technologies médicales

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