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“ BioBrowser: A Framework for Fast Protein Visualization ”

IEEE VGTC Symposium on Visualization (2005). “ BioBrowser: A Framework for Fast Protein Visualization ”. Andreas Halm, Lars Offen, Dieter Fellner (TU Braunschweig). Overview. Existing tools Motivation BioBrowser Overall concepts Different visualization styles Future work Live Demo.

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“ BioBrowser: A Framework for Fast Protein Visualization ”

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  1. IEEE VGTC Symposium on Visualization (2005) “BioBrowser: A Framework for Fast Protein Visualization” Andreas Halm, Lars Offen, Dieter Fellner (TU Braunschweig)

  2. Overview • Existing tools • Motivation • BioBrowser • Overall concepts • Different visualization styles • Future work • Live Demo

  3. Existing Tools • Visualization Tools • RasMol, Chimera, PyMol, Yasara, and others • Modeling Tools • VMD (Visual Molecular Dynamics), NAMD (Scalable Molecular Dynamics), ProtoShop (Interactive Protein Manipulation), etc. • Database Tools • BLAST, FASTA (search for similar structures)

  4. Motivation • Increasing number of structurally fully analyzed molecules • Many different sources of information, e.g. • Protein database • UniProt • GenomeNet • Provide a tool, which integrates this information into the 3D structure of the molecule … (where it really belongs)

  5. BioBrowser - Goals • Provide an integrated access and visualization tool for existing information sources • Challenges: • Visualization (make access as smooth as possible) • Support all common visualization styles • Interactive presentation of huge datasets • Keep precomputed data to a minimum • Integration of the information • Interaction with existing tools for data collection • Integrate collected information into 3D space

  6. Overall Concepts I • Visualization of huge data sets in real time • Just-in-Time generation of the geometry • Reduction of geometry through • Level-of-Detail • Billboarding • Subdivision-Approaches • Use of modern GPU Features • Minimizing precomputed vis-related data • Designing/Use of fast algorithms • Data (e.g. solvent surface geometry) can be made available in real time

  7. Overall Concepts II • Ensure Extensibility • Compact Interface for plugins to integrate new modules (which also supports) • Communication between the different modules • Platform independent • No usage of platform-dependent libraries, like MFC • Use of wxWidgets • Version for: Windows, Linux, Cave, Mozilla/IE-Plugin, PDA (work in progress)

  8. Visualization Styles

  9. LOD-Meshes • Modeled polytopesSubdivision Surfaces Decreasing Geometry Billboards Decreasing GPU functions Adding depth Texture =>Depth sprites • Fully GPU rendered • Ray-shootingon the GPU[Klein&Ertl 2004] Different approaches

  10. Ball and Stick • Spheres don’t intersect and the bonds intersect them in a predictable manner=> use billboards, results in four vertices per billboard • If graphics board is capable of vertex/fragment shaders use a ray-shooting shader => only one vertex per atom or bond

  11. Spacefill • Using van der Waals radius for atoms • Different approaches (GPU capability) • LOD-Meshes • Depth sprites • Fully GPU rendered

  12. Ribbons • Represents the structure of the backbone • Cα-atoms used for position and appearance • Three different kinds: • Helices, -Strands, turns

  13. Ribbons – Technique • Coarse base mesh • Build quads • Subdivision usingcombined BReps (polygonal faces + Catmull/Clark) • Fine tuning of subdivision level • Curvature, projected size, idle time

  14. Surfaces • What are molecular surfaces? • Instead of using fixed resolution (like Marching Cubes), use subdivision surfaces • Leads to both: • high quality visualization • interactivity

  15. Surfaces – Calculation • Calculation: • Molecule • Spacefill • Reduced Surfaces • Base mesh • Subdivision surfaces

  16. Structural Lens • Combine different visualization styles using their respective technique • Improve understanding which substructures define the surface and, therefore, determine the molecule’s function

  17. Future Work • Integrate common tools (e.g. as plug-ins) • Sequence-analysis/alignment • Blast • FASTA • Structure definition • DSSP • Embed additional bio-information, collected from internet or local databases into 3D-structure

  18. Credit The BioBrowser results from a collaboration project (funded by the German Research Foundation, DFG) between the • Institute of Computer Graphics, TU Braunschweig and • Structural Biology,Ges. f. Biotechnologische Forschung (GBF), D. Heinz, G. Dieterich, J. Reichelt

  19. Live Demo Demo

  20. Thank you for your attention!

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