Opportunities for actuated tangible interfaces to improve protein study

ABSTRACT

We outline strategies for actuated tangible user interfaces (TUIs) to improve the study of proteins. Current protein study tools miss fundamental biology concepts because graphical and symbolic interfaces do not allow users to intuitively manipulate complex physical forms. Actuated, tangible tools may enhance understanding at all levels of protein study. To advance TUI awareness of protein study, we present an overview of protein concepts and current protein study tools. Thirty-six protein researchers, engineers, professors and students recommend design guidelines for tangible interfaces in protein study, and we outline research directions for TUIs to improve protein study at all educational levels.

REFERENCES

• 1: Berzelius, Jöns Jakob, Baron. The Columbia Encyclopedia, Columbia University Press, New York, NY, 2001--07.
• 2: Berman, H., Henrick, K. and Nakamura, H. Announcing the worldwide Protein Data Bank. Nature Structural Biology, 10 (12). 980--980.
• 3: Murat Cenk Çavuşoğlu , David Feygin , Frank Tendick, A critical study of the mechanical and electrical properties of the PHANToM haptic interface and improvements for high-performance control, Presence: Teleoperators and Virtual Environments, v.11 n.6, p.555-568, December 2002 [doi>10.1162/105474602321050695]
• 4: Jacques Cohen, Bioinformatics—an introduction for computer scientists, ACM Computing Surveys (CSUR), v.36 n.2, p.122-158, June 2004 [doi>10.1145/1031120.1031122]
• 5: Cruz-Neira, C., Langley, R., & Bash, P. A. (1996). VIBE: A virtual biomolecular environment for interactive molecular modeling. Computers & Chemistry, 20(4), 469--475.
• 6: Paul Dourish, Implications for design, Proceedings of the SIGCHI conference on Human Factors in computing systems, April 22-27, 2006, Montréal, Québec, Canada [doi>10.1145/1124772.1124855]
• 7: Alexandre Gillet , Michel Sanner , Daniel Stoffler , Arthur Olson, Tangible Augmented Interfaces for Structural Molecular Biology, IEEE Computer Graphics and Applications, v.25 n.2, p.13-17, March 2005 [doi>10.1109/MCG.2005.47]
• 8: Hsin, J., Arkhipov, A., Yin, Y., Stone, J.E., & Schulten, K. (2008). Using VMD -- an introductory tutorial. Current Protocols -- Bioinformatics, 5: Unit 5.7.
• 9: Hiroshi Ishii , Brygg Ullmer, Tangible bits: towards seamless interfaces between people, bits and atoms, Proceedings of the SIGCHI conference on Human factors in computing systems, p.234-241, March 22-27, 1997, Atlanta, Georgia, United States [doi>10.1145/258549.258715]
• 10: Kendrew, J.C., Bodo, G., Dintzis, H.M., Parrish, R.G., Wyckoff, H. and Phillips, D.C. A Three-Dimensional Model of the Myoglobin Molecule Obtained by X-Ray Analysis. Nature, 181 (4610). 662--666.
• 11: Vincent LeClerc , Amanda Parkes , Hiroshi Ishii, Senspectra: a computationally augmented physical modeling toolkit for sensing and visualization of structural strain, Proceedings of the SIGCHI conference on Human factors in computing systems, April 28-May 03, 2007, San Jose, California, USA [doi>10.1145/1240624.1240744]
• 12: David Levine , Michael Facello , Philip Hallstrom , Gregory Reeder , Brian Walenz , Fred Stevens, Stalk: An Interactive System for Virtual Molecular Docking, IEEE Computational Science & Engineering, v.4 n.2, p.55-65, April 1997 [doi>10.1109/99.609834]
• 13: McGill, G. Molecular Movies... Coming to a Lecture near You. Cell, 133 (7). 1127--1132.
• 14: Michael Park , Sachin Chitta , Alex Teichman , Mark Yim, Automatic Configuration Recognition Methods in Modular Robots, International Journal of Robotics Research, v.27 n.3-4, p.403-421, March 2008 [doi>10.1177/0278364907089350]
• 15: Purves, W.K., Sadava, D., Orians, G.H. and Heller, H.C. Life, the science of biology. W.H. Freeman & Company, Gordonsville, VA, 2000.
• 16: Hayes Solos Raffle , Amanda J. Parkes , Hiroshi Ishii, Topobo: a constructive assembly system with kinetic memory, Proceedings of the SIGCHI conference on Human factors in computing systems, p.647-654, April 24-29, 2004, Vienna, Austria [doi>10.1145/985692.985774]
• 17: K. Salisbury , D. Brock , T. Massie , N. Swarup , C. Zilles, Haptic rendering: programming touch interaction with virtual objects, Proceedings of the 1995 symposium on Interactive 3D graphics, p.123-130, April 09-12, 1995, Monterey, California, United States [doi>10.1145/199404.199426]
• 18: Sayle, R.A. and Milner-White, E.J. RASMOL: biomolecular graphics for all. Trends in Biochemical Sciences, 20 (9). 374--376.
• 19: Michael Philetus Weller , Ellen Yi-Luen Do , Mark D Gross, Posey: instrumenting a poseable hub and strut construction toy, Proceedings of the 2nd international conference on Tangible and embedded interaction, February 18-20, 2008, Bonn, Germany [doi>10.1145/1347390.1347402]
• 20: Jingkai Yu , Farshad Fotouhi, Computational Approaches for Predicting Protein---Protein Interactions: A Survey, Journal of Medical Systems, v.30 n.1, p.39-44, February 2006 [doi>10.1007/s10916-006-7402-3]

INDEX TERMS

Primary Classification:
  H. Information Systems
  H.5 INFORMATION INTERFACES AND PRESENTATION (I.7)
      H.5.2 User Interfaces (D.2.2, H.1.2, I.3.6)
          Subjects: Interaction styles (e.g., commands, menus, forms, direct manipulation)

Additional Classification:
  J. Computer Applications
  J.3 LIFE AND MEDICAL SCIENCES
      Subjects: Biology and genetics

General Terms:
Design, Human Factors

Keywords:
actuation, education, tangible user interface