From big data to insights: opportunities and challenges for TEI in genomics

ABSTRACT

The combination of advanced genomic technologies and computational tools enables researchers to conduct large-scale experiments that answer biological questions in unprecedented ways. However, interaction tools in this area currently remain immature. We propose that tangible, embedded, and embodied interaction (TEI) offers unique opportunities for enhancing discovery and learning in genomics. Also, designing for problems in genomics can help move forward the theory and practice of TEI. We present challenges and key questions for TEI research in genomics, lessons learned from three case studies, and potential areas of focus for TEI research and design.

References

1. Anderson, M. L. 2003. Embodied cognition: A field guide. Artificial Intelligence, 149: 91--130
2. Arnstein, L., Hung, C.-Y., Franza, R., Zhou, Q. H., Borriello, G, Consolvo, S., Su, J. 2002. Labscape: A Smart Environment for the Cell Biology Laboratory. In IEEE Pervasive Computing Magazine, 1(3). 13--2.
3. Bolchini, D., Finkelstein, A., Perrone, V., Nagl, S. 2009. Better bioinformatics through usability analysis, Bioinformatics, 25(3), 406--12, February 2009.
4. Brooks, F. P., Ouh-Young, M., Batter, J. J., Jerome Kilpatrick, P. 1990. Project GROPE: haptic displays for scientific visualization. In Proc. of SIGGRAPH'90, 177--185.
5. Bourzak, K. 2008. Biologists Enlist Online Gamers, Technology Review, MIT Press.
6. Carlson R. H. 2010. Biology is Technology, MIT Press.
7. Chin L, Hahn WC, Getz G, Meyerson M. 2011. Making sense of cancer genomic data. Genes Dev. 25:534--555.
8. Fjeld, M., Fredriksson, J., Ejdestig, M., Duca, F., Bötschi, K., Voegtli, B., Juchli, P. 2007. Tangible user interface for chemistry education: comparative evaluation and re-design. Proc. CHI'07, ACM, 805--808.
9. Gillet, A., Sanner, M., Stoffler, D., Olson, A. 2005. Tangible augmented interfaces for structural molecular biology. IEEE Comp. Graphics & Applications, 25(2): 13--17.
10. Gray, J., Liu, D., Nieto-Santisteban, M., et al. 2005 Scientific Data Management in the Coming Decade. Proc. SIGMOD'05.
11. Han K., M. Konkel, J. Xing, et al. 2007. Mode and tempo of Old World monkey retrotransposon evolution: a glimpse through the Rhesus macaque genome. Science, v316.
12. Horn, M. S., Tobiasz, M., Shen, C. 2009. Visualizing Biodiversity with Voronoi Treemaps. Proc. Sixth International Symposium on Voronoi Diagrams in Science and Engineering, Copenhagen, Denmark. June 23--26, 2009.
13. Hornecker, E., Jacob, R. J. K., Hummels, C., Ullmer, B., Schmidt, A., van den Hoven, E., and Mazalek, A. 2008. TEI Goes On: Tangible and Embedded Interaction, IEEE Pervasive Computing, vol. 7, no. 2, pp. 91--96.
14. Hornecker, E., Marshall, P., Dalton, N. S., Rogers, Y. 2008. Collaboration and Interference: Awareness with Mice or Touch Input. Proc. ACM CSCW Conference.
15. Kuznetsov, S., Taylor, A. S., Paulos, E., DiSalvo, C., Hirsch, T. 2012. (DIY)biology and opportunities for HCI. Proc. DIS '12.
16. Locke, D., Hillier, L., Warren, W., et al. 2011. Comparative and demographic analysis of orangutan genomes. Nature, 469:529--533.
17. Mackay W. E, Pothier G, Letondal C, Boegh K, Sorensen H. E., 2002. The missing link: augmenting biology laboratory notebooks. Proc. UIST '02.
18. Marcus, A. D. 2011. Family Pioneers in Exploration of the Genome, WSJ Health, September 2011.
19. Mardis, E. 2008. The impact of next-generation sequencing technology on genetics. Trends in Genetics, 24(3), 133--141.
20. Marshall, P., Hornecker, E., Morris, R., Dalton, N., Rogers, Y. 2008. When the Fingers Do the Talking: a Study of Group Participation with Varying Constraints to a Tabletop Interface. Proc. Tabletop 08, 37--44.
21. Mirel, B. 2009. Supporting cognition in systems biology analysis: findings on users' processes and design implications, J Biomed Discov Collab, 27(2),153--155, February 2009.
22. Nersessian, N. J. 2002. The cognitive basis of model-based reasoning in science. The cognitive basis of science. Carruthers, Stich, Siegal, Eds. Cambridge U. Press: 133--153.
23. Nersessian, N. J. 2008. Creating scientific concepts. Cambridge, MA, MIT Press.
24. Nielsen C., et al. 2010. Visualizing genomes: techniques and challenges. Nat. Methods. 7:S5--S15.
25. Okada, T., Simon, H. A. 1997. Collaborative discovery in a scientific domain. Cognitive Science, 21 (2), 109--146.
26. Patten, J., Ishii, H. 2000. A Comparison of Spatial Organization Strategies in Graphical and Tangible User Interfaces, Proc. DARE'00, 41--50.
27. Rhesus Macaque Genome Sequencing and Analysis Consortium. 2007. The Rhesus macaque genome sequence informs biomedical and evolutionary analyses. Science, v316, 222--234, April 13. (Cover article.)
28. Rittle-Johnson, B. Star, J. R. 2007. Does comparing solution methods facilitate conceptual and procedural knowledge? An experimental study on learning to solve equations. Journal of Educational Psychology, 99(3): 561--574.
29. Ryall, K., Forlines, C., Shen, C., Morris, M. R., Everitt, K. 2006. Experiences with and Observations of Direct-Touch Tabletops. Proc. IEEE Tabletop'06.
30. Saraiya, P., North, C., Duca, K. 2005. An insight-based methodology for evaluating bioinformatics visualizations, Visualization and Computer Graphics, 11(4), 443--456.
31. Schkolne, S., Ishii, H., Schroder, P. 2004. Immersive design of DNA molecules with a tangible interface, Visualization, IEEE, 227--234.
32. Schneider, B., Strait, M., Muller, L., Elfenbein, S., Shaer, O., Shen, C. 2012. Phylo-Genie: engaging students in collaborative 'tree-thinking' through tabletop techniques. Proc. CHI'12.
33. Scott, S. D., Grant, K. D., Mandryk, R. L. 2003. System guidelines for co-located, collaborative work on a tabletop display. Proc. ECSCW'03.
34. Shaer, O., Hornecker, E. 2010. Tangible User Interfaces: Past, Present, and Future Directions, Foundations and Trends in Human-Computer Interaction, 3(1--2), April 2010.
35. Shaer, O., Kol, G., Strait, M., Fan, C., Grevet, C., Elfenbein, S. 2010. G-nome surfer: a tabletop interface for collaborative exploration of genomic data. Proc. CHI'10.
36. Shaer, O., Strait, M., Valdes, C., Feng, T., Lintz, M., Wang, H. 2011. Enhancing Genomic Learning through Tabletop Interaction. Proc. CHI'11.
37. Shaer, O., Strait, M., Valdes, C., Wang, H., Feng, T., Lintz, M., Ferreirae, M. Grote, C., Tempel, K., Liu, S. 2012. The Design, Development, and Deployment of a Tabletop Interface for Collaborative Exploration of Genomic Data, International Journal of Human-Computer Studies.
38. Singer, S. R., Hilton M. L., Schweingruber, H. A. 2005. America's lab report: investigations in high school science, National Research Council.
39. Tabard A, Mackay W. E., Eastmond, E. 2008. From individual to collaborative: the evolution of prism, a hybrid laboratory notebook. Proc. CSCW '08.
40. Tabard, A., Hincapié-Ramos, J-D., Esbensen, M., Bardram, J. E. 2011. The eLabBench: an interactive tabletop system for the biology laboratory. Proc. ITS '11.
41. Tang, A., Neustaedter, C., Greenberg, S. 2006. Videoarms: Embodiments for mixed presence groupware. Proc. HCI '06.
42. Tuddenham, P., Robinson, P. 2007. Distributed tabletops: Supporting remote and mixed-presence tabletop collaboration. Proc. TABLETOP '07.
43. Ullmer, B. 2012. Entangling space, form, light, time, computational STEAM, and cultural artifacts. Interactions, 19(4): 32--39.
44. Ullmer, B., Kim, E., Kilian, A., Gray, S., Ishii, H. 2001. Strata/ICC: physical models as computational interfaces. CHI '01 extended abstracts.
45. Veretnik, S., Fink, J., Bourne, P. 2008. Computational biology resources lack persistence and usability, PLoS computational biology, 7(4), July 2008.
46. Wigdor, D., Jiang, H., Forlines, C., Borkin, M., Shen, C. 2009. WeSpace: The Design, Development and Deployment of a Walk-Up and Share Multi-Surface Visual Collaboration System. Proc. CHI '09, Boston, MA.
47. Wilson, M. 2002. Six views of embodied cognition. Psychonomic Bulletin and Review, 9(4): 625--636.
48. Wilson, S. 2002. Information arts: Intersections of art, science, and technology. Cambridge, MA, MIT Press.
49. Wu, A., Caspary, E., Yim, J.-B., Mazalek, A., Chandrasekharan, S., Nersessian, N. J. 2011. Kinesthetic pathways: A tabletop visualization to support discovery in systems biology. Proc. Creativity and Cognition, 21--30.
50. Yeh, R., Liao, C., Klemmer, S., Guimbretière, F., Lee, B., Kakaradov, B., Stamberger, J., Paepcke, A. 2006. ButterflyNet: a mobile capture and access system for field biology research, Proc. CHI'06, 571--580.

Index Terms

• Applied computing

  • Life and medical sciences

    • Computational biology

    • Genetics

    • Systems biology

• Human-centered computing

  • Human computer interaction (HCI)

    • Interaction devices

      • Touch screens

    • Interaction paradigms