Improving Collaborative Visualization of Structural Biology

  • Aaron Bryden
  • George N. PhillipsJr.
  • Yoram Griguer
  • Jordan Moxon
  • Michael Gleicher
Part of the Lecture Notes in Computer Science book series (LNCS, volume 6938)


Structural biology is the study of how molecular shape, chemistry and physics connect to biological function. This work is inherently multidisciplinary and co-located group discussions are a key part of the work as participants need to refer to and study visualizations of the molecule’s shape and properties. In this paper, we present the design and initial assessment of CollabMOL, a collaborative molecular visualization tool specifically designed to support small to medium size groups working with a large stereo display. We present a task analysis for co-located collaborative work in structural biology in which we find shortcomings in existing practice as well as key requirements of an appropriate solution. In this paper we present our design of this solution and an observation based user study to validate its effectiveness. Our design incorporates large stereo display support, commodity input devices and displays, and an extension to an existing molecular visualization tool.


Task Analysis Structural Biology Collaborative System Collaborative Discussion Molecular Visualization 
These keywords were added by machine and not by the authors. This process is experimental and the keywords may be updated as the learning algorithm improves.


Unable to display preview. Download preview PDF.

Unable to display preview. Download preview PDF.


  1. 1.
    O’Donoghue, S.I., Goodsell, D.S., Frangakis, A.S., Jossinet, F., Laskowski, R.A., Nilges, M., Saibil, H.R., Schafferhans, A., Wade, R.C., Westhof, E., Olson, A.J.: Visualization of macromolecular structures. Nature Methods 7, s42–s55 (2010)CrossRefGoogle Scholar
  2. 2.
    Lesk, A.M., Hardman, K.D.: Computer-generated schematic diagrams of protein structures. Science 216, 539–540 (1982)CrossRefGoogle Scholar
  3. 3.
    Sanner, M., Olsen, A., Spehner, J.C.: Fast and robust computation of molecular surfaces. In: Proceedings of the 11th ACM Symposium on Computational Geometry, pp. C6–C7. ACM, New York (1995)Google Scholar
  4. 4.
    Tarini, M., Cignoni, P., Montani, C.: Ambient occlusion and edge cueing for enhancing real time molecular visualization. IEEE Transactions on Visualization and Computer Graphics 12, 1237–1244 (2006)CrossRefGoogle Scholar
  5. 5.
    Cipriano, G., Gleicher, M.: Molecular surface abstraction. IEEE Transactions on Visualization and Computer Graphics 13, 1608–1615 (2007)CrossRefGoogle Scholar
  6. 6.
    Humphrey, W., Dalke, A., Schulten, K.: VMD – Visual Molecular Dynamics. Journal of Molecular Graphics 14, 33–38 (1996)CrossRefGoogle Scholar
  7. 7.
    Pettersen, E.F., Goddard, T.D., Huang, C.C., Couch, G.S., Greenblatt, D.M., Meng, E.C., Ferrin, T.E.: UCSF Chimera–a visualization system for exploratory research and analysis. Journal of Computational Chemistry 25, 1605–1612 (2004)CrossRefGoogle Scholar
  8. 8.
    Akkiraju, N., Edelsbrunner, H., Fu, P., Qian, J.: Viewing geometric protein structures from inside a cave. IEEE Computer Graphics and Applications 16, 58–61 (1996)CrossRefGoogle Scholar
  9. 9.
    Su, S., Loftin, R., Chen, D., Fang, Y., Lin, C.: Distributed collaborative virtual environment: Paulingworld. In: Proceedings of the 10th International Conference on Artificial Reality and Telexistence, pp. 112–117 (2000)Google Scholar
  10. 10.
    Forlines, C., Lilien, R.: Adapting a single-user, single-display molecular visualization application for use in a multi-user, multi-display environment. In: Proceedings of the Working Conference on Advanced Visual Interfaces, AVI 2008, pp. 367–371. ACM, New York (2008)Google Scholar
  11. 11.
    Leblanc, A., Kalra, P., Thalmann, N.M., Thalmann, D.: Sculpting with the ”ball & mouse” metaphor. In: Proceedings of Graphics Interface 1991, pp. 152–159 (1991)Google Scholar
  12. 12.
    Balakrishnan, R., Kurtenbach, G.: Exploring bimanual camera control and object manipulation in 3d graphics interfaces. In: Proceedings of the SIGCHI Conference on Human Factors in Computing Systems: the CHI is the Limit, CHI 1999, pp. 56–62. ACM, New York (1999)Google Scholar
  13. 13.
    Bowman, D.A., Kruijff, E., LaViola, J.J., Poupyrev, I.: 3D User Interfaces: Theory and Practice. Addison-Wesley Professional, Reading (2004)Google Scholar
  14. 14.
    Frolov, P., Matveyev, S., Göbel, M., Klimenko, S.: Using kalman filter for natural hand tremor smoothing during the interaction with the projection screen. In: Workshop Proceedings VEonPC 2002, pp. 94–101 (2002)Google Scholar

Copyright information

© Springer-Verlag Berlin Heidelberg 2011

Authors and Affiliations

  • Aaron Bryden
    • 1
  • George N. PhillipsJr.
    • 1
  • Yoram Griguer
    • 1
  • Jordan Moxon
    • 1
  • Michael Gleicher
    • 1
  1. 1.University of WisconsinMadisonUSA

Personalised recommendations