EuroVis 2005 1Computer Graphics, TU Braunschweig
“BioBrowser: A Framework for Fast Protein Visualization”
Andreas Halm, Lars Offen, Dieter Fellner (TU Braunschweig)
IEEE VGTC Symposium on Visualization (2005)
EuroVis 2005 2Computer Graphics, TU Braunschweig
Overview
Existing tools Motivation BioBrowser
Overall concepts Different visualization styles
Future work Live Demo
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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)
EuroVis 2005 4Computer Graphics, TU Braunschweig
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)
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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
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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
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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)
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Visualization Styles
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Different approachesD
ecre
asin
g G
eom
etry
Dec
reas
ing
GP
U f
unct
ions
LOD-Meshes
Modeled polytopesSubdivision Surfaces
Adding depth Texture =>Depth sprites
Fully GPU rendered
Ray-shooting on the GPU[Klein&Ertl 2004]
Billboards
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Ball and Stick Spheres don’t intersect and
the bonds intersect them in a predictable manner=> use billboards,
results in four verticesper billboard
If graphics board is capable of vertex/fragment shaders use a ray-shooting shader => only one vertex per
atom or bond
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Spacefill
Using van der Waals radius for atoms
Different approaches (GPU capability)
LOD-Meshes Depth sprites Fully GPU rendered
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Ribbons
Represents the structure of the backbone
Cα-atoms used for
position and appearance
Three different kinds: Helices, -Strands,
turns
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Ribbons – Technique
Coarse base mesh Build quads
Subdivision usingcombined BReps (polygonal faces + Catmull/Clark)
Fine tuning of subdivision level
Curvature, projected size, idle time
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Surfaces
What are molecular surfaces?
Instead of using fixed resolution (like Marching Cubes), use subdivision surfaces
Leads to both: high quality
visualization interactivity
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Surfaces – Calculation
Calculation: Molecule Spacefill Reduced
Surfaces Base mesh Subdivision
surfaces
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Structural Lens
Combine different visualization styles using their respective technique
Improve understanding which substructures define the surface and, therefore, determine the molecule’s function
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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
EuroVis 2005 20Computer Graphics, TU Braunschweig
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
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Live Demo
Demo
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Thank you for your attention!