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Alternative Representations of Biological Complexes: Navigating Complexity for Enhanced Understanding

Biologists aim to analyze and visualize large structures while accessing atomic details efficiently. Challenges include complexity, seekable file formats, LOD control, and new visual representations. Explore the evolving complexity roadmap and future representation strategies to decode biological intricacies effectively.

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Alternative Representations of Biological Complexes: Navigating Complexity for Enhanced Understanding

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  1. Alternative Representations for Biological Complexes:Decreasing Complexity while Increasing Knowledge John L. Morelandmoreland@sdsc.edu 1GRL

  2. Challenges • Biologists want to analyze and visualize larger structures but still drill down to the atomic level • Need hierarchical and spatial data models • Size of data may preclude reading complete atomic-level data into memory at once • Need seekable file formats and spacially indexed DBs • Complexity of structure may preclude rendering all at the atomic level even with fast GPUs • Need LOD control (both automatic and authored) • Need alternative and new visual representations

  3. Structure Complexity Roadmap (or, Train Wreck?) Non-seekable file formats, non-hierarchical data structures, and brute force rendering may not work any more… Structure Atoms Atom 1x10e0 Residue/ChemComp 1x10e1 S.Structure Fragment 1x10e2 Chain 1x10e3 Asymetric Unit 1x10e4 Biological Unit 1x10e5 <-- You are here... Macromolecular Complex 1x10e6 <-- How do we go bigger? Organelle 1x10e9 <-- Eek! Cell 1x10e11 Tissue 1x10e17 Organ 1x10e23 Organism (Human) 1x10e27 <-- Can we get here? 1HTQ mmCIF: 105MB 1 million atoms

  4. Complexity Problems • Data • 1HTQ.cif • 1M atoms, 105MB • "Complexes" 10-100x • 10-100M atoms, 1-10GB RAM+ (won't fit in PC RAM) • Graphics • 200 polys/atom, 60 polys/bond • NVidia FX3400, 25M polys/sec, but at 30fps we can only render 1M polygon scenes • 2.6M-26M polygons (can't render)

  5. Controlling Rendering Complexity • Complexity =~ (A+B)*R*G • A = number of Atoms • B = Number of Bonds • R = Representation Constant • G = Graphics Rendering Cost • Assume maximum detail is fixed by A and B • Have to pick SOME representation that costs R (may be a fraction) • Can control G by varying rendering detail and style

  6. RepresentationIssues • Data Representations • File Formats • PDB and mmCIF are not seekable (hard to find/read subsets) • Consider seekable, hierarchical, and perhaps binary file formats • Consider pre-indexing for common access patterns (for example, C-alpha atoms, hierarchical subsets) • Consider toolkit specific seekable disk caches (don't have to toss existing formats) • Databases • Consider spacial indexing and queries • Visual Representations • Need new representations beyond backbones, ribbons, and even Connolly type surfaces which reduce rendering complexity but more than an envelope

  7. Traditional Visual Representations • Atoms, Bonds, Residues • Ball-and-Stick • CPK Spheres • Chains, Secondary Structures, Asymetric Units • Backbone Traces • Ribbon / Cartoon Diagrams • Biologically Active Structures and Beyond • Already getting too big for these representations

  8. Bake-Off StructuresMBT Renderings 1FFK 1IBM 1GRL 1UF2

  9. Bake-Off StructuresObservations • Visual Representations • Chains = S.Structure Cartoons • DNA, Ligands = Ball-And-Stick • Can see silhouette and clefts, but… • Too cluttered • Atomic representation useless • Inefficient to render unseen detail • Does it reveal anything useful?

  10. What Detail is Needed? • Need input from domain scientists • What data attributes and biological concepts need to be represented? • Active Sites, Protein-Ligand Binding • Crystallographic Symmetry • Biological Complex Features? • Need meaningful visual representations for even larger biomolecular complexes! • We can also cheat on representation detail at rendering time…

  11. LOD HierarchyAtoms/Bonds

  12. LOD HierarchyS.Structure Cartoons

  13. LOD HierarchyNew Representations… • As new visual representations of biomolecular complexes are developed, think about simplified variations for rendering

  14. Intelligent use of Detail For some special cases, we can apply detail where its needed

  15. Summary • Data Representations • Need seekable hierarchical file formats and spacially queryable DBs • Need hierarchical and spatial data models • Visual Representations • Need new visual representations which reveal useful information about large structural features • Need LOD control • Automatic view-based rendering simplification • Hierarchical bounding polytopes? • Progressive refinement techniques?

  16. Questions? ?

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