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BioBrowser: A Comprehensive Framework for Fast Protein Visualization

The BioBrowser project aims to provide an integrated access and visualization tool for protein data. It addresses the increasing number of structurally analyzed molecules from various information sources like protein databases and genomic data. The framework incorporates innovative visualization techniques, supports all common styles, and allows real-time visualization of large datasets. BioBrowser's architecture ensures extensibility, a compact interface for plugins, and compatibility across platforms. Future work includes integration with commonly used tools for enhanced functionality.

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BioBrowser: A Comprehensive 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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