Visualization, Animation, and Integration of Biological Complexes

1. Visualization, Animation, and Integration of Biological Complexes Matthew Dougherty NCMI/BCM 10/11/2003

2. VisualizationThe visual experience of exploration, disassembly, and integration as a means of introspection and insight.

3. AnimationThe temporal presentation of a sequence of visualization images.

4. Mark Twain • Lies • Damnable lies • Statistics • (visualization & animation)

5. Viz History at NCMI • 2D images: parallel I/O • 3D structures: SGI, isosurfacing, 32**3 • Remedial segmentation • Stereo lithography • Scientific animation • Integration: custom s/w • Integration: other tools • Scientific Animation & Integration Library

6. Viz software at NCMI • Software used: Iris Explorer, Vis5D, Chimera, O,Ribbons • 13 years using Iris Explorer • Looked at: AVS, DX Explorer, VTK, Amira, IDL, Alias, Maya, Softimage, 3D Studio max, Houdini, Lightwave

7. Comments about Iris Explorer • Iris Explorer +: parallel, extensible, cheap • Iris Explorer -: stagnant, bugs • 32 bit addressing, shared memory limits data to 500**3, floating point • Maximum addressing space of 96GB: 500MB(shared),1.5GB segments*64 • Graphics: open Inventor/openGL, interactive use below 5M polygons • Available on SGI, LINUX, IBM, MS

8. Critical decisions • 3D visualization was essential for research • Animation was essential for presentations • Animation must be driven by the researchers’ visualizations. Animation s/w doing SciViz vs. SciViz s/w doing animation • Adherence to international standards such as X windows and MPEG • Use of SGI equipment • Transition to LINUX

9. Observations • Project management is absolutely necessary for animation production; s/w design requirement. • Project management is necessary for visualization. And the rest of it. • Animation started out as a visual illusion to make 2D look like 3D. Later we realized that storytelling eclipsed this.

10. Observations • Viz industry is being driven by the entertainment industry • Generic sciViz packages have peeked • Buying custom s/w tools to support structural biology will be difficult, it’s a small market • Repeatability of visualization is an Achilles heel of the science

11. Observations • Project and data management are becoming the limiting factors to research productivity • Interactivity and intuitive methodologies have a positive effect on researchers getting their work done • Better human/machine interfaces are needed

12. Observations • Design, prototyping, redesign, extensibility, testing, documentation, life cycle planning, training, and maintenance take time, effort and money. • Videoconferencing will be essential for improved research collaboration and viz software development • Need to redouble the efforts to keep up with relevant science, technology and arts so it can be utilized for sciViz

13. What needs to visualized? • Raw scientific data, various disciplines • Interpretations of the metadata • Theoretical and evolving models • The story, the importance of the effort • Imagination

14. Future directions • Increased use of Python • Integration with Viper, Chimera, VMD, PyMol, Amira & OME • Utilization of HDF for data access • Utilization of XML for data interchange • Utilization of UML for project & data organization • Utilization of EBI’s EMDEP • Expansion of video collaboration • Development of human interfaces (spaceball, touchscreen, & stereo vision) • Revaluation of sciViz/animation methodology • Workflow management

15. Examples P22 Rota Microtubule Ribosome References E. Tufte, Visual Explanations, Graphics Press, 1997 P. & M. Keller, Visual Cues, IEEE Press, 1992 J. Vince, 3D Computer Animation, Addison-Wesley, 1992 E. Tufte, The Visual Display of Quantitative Information, Graphics Press, 1983 Isaac Kerlow, The Art of 3D Computer Animation and Imaging, Van Norstrand Reinhold, 1996 S. Katz, Film Directing Shot by Shot, Michael Wiese Productions, 1991 For further information contact me at matthewd@BCM.TMC.EDU Research supported by NCRR/NIH, NSF & the Keck Foundation