FOCUS K3D AWG Medicine and Bioinformatics


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FOCUS K3D is a Coordination Action (CA)which aims at promoting the adoption of best-practices for the use of semantics in 3D content modelling and processing. This slide set gives an overview of the Application Working Group (AWG) Medicine and Bioinformatics.

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FOCUS K3D AWG Medicine and Bioinformatics

  1. 1. AWG Medicine and Bioinformatics F. Cazals INRIA
  2. 2. 3D and Knowledge in Medicine and Bioinformatics Medicine Geometric Modeling Diagnostic Therapy planning Surgery Radiotherapy Legal medicine
  3. 3. 3D and Knowledge in Medicine and Bioinformatics Biology Docking Molecular surfaces and volumes Modeling molecular interfaces Modeling pockets and channels Databases (e.g. PDB), functional classifications Folding Conformers Atomic environments Folding styles
  4. 4. Geometry and Knowledge: Synergy Model: geometry and knowledge Geometry: At organ level: tissues (volumes and surfaces), interfaces (surfaces), relative positioning. At molecule level: atoms (locations, shape), bonds, secondary structure, domains. Knowledge: Anatomy, physiological and pathological parameters. Chemical and interaction types, affinity specificity of interactions.
  5. 5. Contacts Medicine #contacts: 20 #questionnaires: 12 Categories Methodology e.g., image segmentation, mesh generation, simulation Application e.g., organ or pathology-specific Integration environment suppliers, medical teams
  6. 6. Contacts Biology #contacts: 20 #questionnaires: 13 Categories Methodology e.g., shape matching and comparison, shape reconstruction Applications folding, docking, drug design Integration environment suppliers, pharma-companies, biological teams
  7. 7. Example Key Players in Medicine Methodology Applied mathematicians: e.g., model design for dynamic heart simulation. Application Electro-physiologist: computer aided diagnostic and recovery after heart attack. Integration Medical team: optimization of pacemaker placement, resection.
  8. 8. Example Key Players in Biology Methodology Biophysicist / applied mathematician: e.g., algorithms for electrostatic calculations (Poisson- Boltzmann)‫‏‬ Application Biophysicist into folding and misfolding (e.g., amyeloid diseases)‫‏‬ Integration Structural Modeling group: from bio-physical measurements to simulations
  9. 9. Scenario in Biomedicine Simulating human articulations: bone resection Prosthesis placement Parameters of interest: contact pressure within the cartilages forces during motion muscle biomechanics Connection to physiology: material properties bone motion and geometry Since the parameters are stored in the ontology, the data process is simplified.
  10. 10. Scenario in Biomedicine Modeling anatomy patient-specific therapy planning e.g., air flow simulation Parameters of interest: segmentation of upper respiratory tract flow, pressure deformations Connection to physiology: material properties geometry of upper respiratory tract mesh generation for simulation
  11. 11. Scenario in Bioinformatics Docking two molecules involves: Homology modeling Rigid body docking Side chain placement Molecular dynamics simulations Parameters of interest: Homology between proteins Known partners Rigid domains within protein Key residues Correlated motions Connections to experiments Directed mutagenesis Affinity and specificity measurements (e.g. BIACORE)
  12. 12. Assessment Case 1: The problem description is complete Key parameters identified Geometric models effective for description and prediction Ex: articulations, zoo of protein folds Ontologies crucial to integrate Synergy needed between geometry, models and ontologies Case 2: Problem partially described Key parameters not yet identified Incomplete knowledge Hazardous extrapolation and prediction Ex: brain modeling, protein folding process Building blocks of models to be elaborated upon Integration will come next