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Journées INRA - INRIA

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

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Journées INRA - INRIA

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

  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 scientists • 1500 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. INRIA FUTURS, Lille Metz Paris Lannion INRIA Rocquencourt LORIA Nancy Strasbourg INRIA FUTURS Saclay IRISA Rennes Besançon Nantes Lyon INRIA Rhône-Alpes Grenoble INRIA FUTURS Bordeaux Marseille Montpellier INRIA Sophia Antipolis Research centers Journées INRA - INRIA

  6. Lille Nancy Rennes Paris-Rocquencourt Saclay Grenoble Bordeaux Sophia Antipolis Research Centers 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 • Understanding and predicting natural processes : meteorology, oceanography, hydrology, glaciology • Social challenges: water resources, risk prevention and management, evolution of the climate, territory planning, 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 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. Biomasse Photosynthèse No stress W. stress Fonction puits Efficience de l’eau Organogénèse Digiplante : GreenLab3 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 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 Brain Heart 200 microns Bladder cells Microvessels & leukocytes Neuro-muscular junctions 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 physiopathology nano ATP micro sarcomeres meso fibers macro INRIA in silico electro- mechanical cardiac model 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 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 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. Very large data Heterogeneous data Distributed data Confidentiality constraints Time constraints Grid computing Parallel computing Semantics grids technologies Semantic web Dedicated computing platforms Exploit massively parallel computing 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 Interpretation (diagnosis) Prediction of evolution Medical Images and Signals Computational Models of human body Geometry Statistics Physics Physiology Therapy planning Therapy simulation Identification (personalization) 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. Digital Environment • Platforms and systems forMonitoring, forecasting, risk management at local and global scalesIntegrating 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 Journées INRA - INRIA

  37. Digital Environment • 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 Journées INRA - INRIA

  38. Digital Environment • 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 Journées INRA - INRIA

  39. Inria Strategic Plan Journées INRA - INRIA

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