1. Welcome to 3D Visualization and the Geowall Christian Educators Annual Fall Conference October 2005 The King’s University College, Edmonton Dr. Brian Martin Dr. Peter Mahaffy The King’s Centre for Visualization in Science

2. The Myth of Visualization as “Seeing is Believing” A Simple Task…  Watch the white team and count the exact number of times the white team passes the ball back and forth

3. Workshop Goals… Acquaint you with current best practices in developing science visualizations Provide you with sufficient technical understanding to set up your own Geowall Provide you with insights into presently available software options to use with Geowall Assist you in applying Geowall technology to your visualization interests Work collectively on understanding the educational application of Geowall The best kept secret

4. The King’s Center for Visualization in Science (KCVS) Explore ways in which visualization (not just computer based) can be used to enhance understanding:  Among students  Among researchers Explore ways to implement visualizations into teaching at both secondary and post secondary levels To work within international communities of scholars researching topics related to visualization

5. KCVS: Past, Present, Future Modular Approach to Physics Project (MAP) 1997 – 2004 Gordon Research Conferences Centres for Research in Youth, Science Teaching and Learning - CRYSTALS

6. Gordon Research Conference on Visualization in Science & Education, Oxford, July 2005 Mahaffy (Chair) Martin (Workshop Leader) Flowing water in SE Jordan NASA Satellite Image

8.  New emphases  Visualization in nanotechnology  Best practices in production and dissemination of educational visualizations  Visualization in genomics and systems biology  Computer graphics / cognitive science interface  Visualization for public understanding of science  Physical models and touch in forming mental models  Geo-Wall 3D visualization applied to other disciplines http://www.grc.org/

9. King’s, KCVS and CRYSTALS 5 year, 200K/a, Mahaffy (co-PI), Martin (management team &co-PI) Project involves U of A, King’s, 3 other post-secondaries, Edmonton Schools, Telus World of Science and others Current projects KCVS will play a role in:  Visualizing Global Climate Change (with NSF)  Ethical Use of Chemicals (with IUPAC) Major role for undergraduate student researcher/programmers

10. Car on a banked roadway Applets that Help the Student Visualize Complex Phenomena

11. Thin Film Interference Applets that Help the Student Visualize Complex Phenomena

12. First … a fast breaking news story

13. Refresher course on polarized light… Plane polarized light – what is it? Simple (and fun!) demos with polarized light  Scotch  Plastics  De-polarizers Tape!

14. I. Geowall – Technical Considerations Uses 2-matched DLP projectors (“left” & “right”) each outputting a plane polarized image rotated 90 0 wrt the other. Screen is “daylite” type – polarization preserving Eyeglasses “decode” left and right eye information – your brain does the rest!

15. Geowall – Technical Considerations Left-channel imageRight-channel image Left channel image is projected through the left channel DLP projector and is plane- polarized as shown Right channel image is projected through the right channel DLP projector and is plane- polarized as shown

16. Geowall – Technical Considerations Projectors are stacked vertically with 3 rotational and translational degrees- of-freedom Computer should be equipped with a video board capable of running 2 monitors Passive stereo – image “stacking” Crude alignment can be achieved using separate monitor windows from each projector

17. Geowall – Technical Considerations Left and Right channel polaroids are placed in front of the lens – avoid touching the lenses as conducted heat will quickly (< 1 hour) degrade filters Final alignment achieved by using stereoviewer and the Geowall alignment image Not quite!BetterGood (not perfect)! Congratulations – you are ready for stereo projection! for stereo projection!

18. II. Software – Creating Stereo Images Two parts:  Creating or capturing L and R channel images  Combining L and R channel images.

19. More on Creating Stereo Images Digital Camera  Two images contain all of the stereo information needed for your brain to produce a stereo pair Translate camera L to R

20. More on Creating Stereo Images 3D Image rendering software  Blender – freeware (outstanding package but steep learning curve)  Bryce (more accessible but not free) Either offset “camera” or scene and render both L and R channel images.

21. Combining Left and Right Channels “Do-it-yourself”:  GIMP (freeware – excellent!)  Fireworks, Photoshop etc Stereo Image Software  Pokescope (low cost < $30USD)

22. III. Free Software that Supports Stereo Projection Chemistry/Biology:  JMOL  Pymol  VMD  Protein Explorer Physics/Astronomy  VPython  Astrowall suite  Wallview

23. IV. Using 3D Projection to Enhance Student Understanding Astronomy:  Understanding phases, eclipses Physics  Magnetic fields around wires Organic Chemistry  Stereo chemistry Biochemistry  DNA, protein structure, etc

24. Visualizing the World Too Small To See: Small Matters Christina deMatteis, University of Nottingham

25. The Importance of Multiple Representations at the Molecular Level Roy Tasker, Univ. Western Sydney Models in Chemistry “The most powerful thing you can do when you’re learning chemistry is to zoom down, in your mind’s eye, to the molecular level and try to imagine what is going on and in a sense, try to understand the personalities of the reactants and products… Having each type of model show a different aspect is ideal. Because then students don’t look at a particular model and say: that’s reality.”

26. "Since garlic hath powers to save from death, bear with it though it makes unsavory breath" Robert of Normandy, 1100 AD Literature Reports Allium sativum Broad spectrum antibacterial activity, including Helicobacter pylori Antifungal activity Antiviral activity Normalization of plasma lipid levels Stimulates lymphocytes and elicits anti-tumor effects Anti-hypertensive effects Bacillus anthracis inhibition?

27. 2D TLC of dichloromethane garlic extract Several compounds inhibit Bacillus subtilis growth 1 st Dimension – Less Polar Solvent 2 nd Dimension–More Polar Solvent Initial Spot

28. Allicin Bioactive Compound: Allicin E. Block.Agnew. Chem. Int. Ed. Engl. 1992, 31, 1135-1178

29. Mode of Action of Allicin  Interferes with microbial cellular function DNA & RNA synthesis Signal transduction & apoptosis  Blocks the active site on sulfhydryl enzymes

30. Investigative laboratories For majors and non-majors

32. from visual import * #simple program to illustrate lunar nodes and eclipse conditions #In this example an eclipse is possible - the line of nodes points at the sun scene.stereo='passive' scene.stereodepth = 1 scene.ambient = 0.005 scene.lights = [vector(1,0,0)] scene.ambient=0.1 orb1=ring(pos=(1,1,1), axis=(0,1,0), radius=50, thickness=0.2, color = color.red) orb2=ring(pos=(1,1,1), axis=(0,1,0.2), radius=50, thickness=0.2) earth = sphere(pos=(1,1,1), radius=5, color=color.blue) #sun = sphere(pos=(500,0,1), radius=15, color = color.yellow) lineofnodes = cylinder(pos=(-50,1,1), axis=(100,0,0), color=color.yellow, radius =0.4) moon = sphere(pos=(50,1,1), radius = 2) angle = 0 delta = 2e-2 while 1: rate(10) angle = delta moon.rotate(angle=angle, axis=(0,1,0), origin=(1,1,1)) #lineofnodes.rotate(angle=angle/100, axis=(0,1,0), origin=(1,1,1)) Example using VPython …easy as this!

33. Resources… Geowall Site: http://geowall.geo.lsa.umich.edu/http://geowall.geo.lsa.umich.edu/ Vpython: http://vpython.org/http://vpython.org/ VMD: http://www.ks.uiuc.edu/Research/vmd/http://www.ks.uiuc.edu/Research/vmd/ Protein Explorer: http://www.umass.edu/microbio/chime/pe/protexpl/frntdoor.htm http://www.umass.edu/microbio/chime/pe/protexpl/frntdoor.htm Gimp: http://www.gimp.org/ Blender: http://blender.org/ Contacts:  Paul Morin @ Geowall (lpaul@umn.edu)lpaul@umn.edu  Brian Martin (brian.martin@kingsu.ca)