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Designing reality-based interfaces for experiential bio-design

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Abstract

Reality-based interfaces (RBIs) such as tabletop and tangible user interfaces draw upon ideas from embodied cognition to offer a more natural, intuitive, and accessible form of interaction that reduces the mental effort required to learn and operate computational systems. However, to date, little research has been devoted to investigating the strengths and limitations of applying reality-based interaction for promoting learning of complex scientific concepts at the college level. We propose that RBIs offer unique opportunities for enhancing college-level science education. This paper presents three main contributions: (1) design considerations and participatory design process for enhancing college-level science education through reality-based interaction, (2) reflections on the design, implementation, and validation of two case studies—RBIs for learning synthetic biology, and (3) discussion of opportunities and challenges for advancing learning of college-level sciences through next-generation interfaces.

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References

  1. (2013) Retrieved from Geneious: http://www.geneious.com

  2. (2013) Retrieved from Ape: http://biologylabs.utah.edu/jorgensen/wayned/ape/

  3. (2013) Retrieved from Genme Compiler: http://www.genomecompiler.com

  4. (2013) Retrieved from Vector Express: http://www.vectorexpress.com

  5. (2013) Retrieved from MIT Parts Registry: http://partsregistry.org/Main_Page

  6. (2013) Retrieved from iBioSim: http://www.async.ece.utah.edu/iBioSim/

  7. (2013) Retrieved from BioBuilder: http://www.biobuilder.org

  8. (2013) Retrieved from International Genetically Engineered Machine (iGEM): http://igem.org/About

  9. (2013) Retrieved from DIY Bio: http://diybio.org

  10. (2013) Retrieved from Sifteo: https://www.sifteo.com/

  11. (2013) Retrieved from The UNAFold Web Server: http://mfold.rna.albany.edu/

  12. (2013) Retrieved from Microsoft PixelSense: http://www.microsoft.com/en-us/pixelsense/default.aspx

  13. Anderson JC (2013) Synthetic Biology Learning trails

  14. Anderson ML (2003) Embodied cognition: a field guide. Artif Intell 149(1):91–130

    Google Scholar 

  15. Andrianantoandro E, Basu S et al (2006) Synthetic biology: new engineering rules for an emerging discipline. Mol Syst Biol 2:0028

    Article  Google Scholar 

  16. Antle A (2007) The CTI framework: informing the design of tangible systems for children. In: TEI. ACM Press, LA, pp 195–202

  17. Antle AN, Wise A (2013) Getting down to details: using learning theory to inform tangibles research and design for children. Interact Comput 25(1):1–20

    Google Scholar 

  18. Antle AN, Droumeva M, Ha D (2009). Hands on what? Comparing children’s mouse-based and tangible-based interaction. In: International conference on interaction design and children. ACM, New York, pp 80–88

  19. Beal J, Lu T, Weiss R (2011) automatic compilation from high-level biologically-oriented programming language to genetic regulatory networks. Plos One 6(8):e22490

    Google Scholar 

  20. Beal J, Weiss R, Densmore D, Adler A, Appleton E, Babb J, Yaman F (2012) An end-to-end workflow for engineering of biological networks from high-level specifications. ACS Synth Biol 1(8):317–331

    Article  Google Scholar 

  21. Beeland WJ (2002) Student engagement, visual learning and technology: can interactive whiteboards help. In: Association of IT for teaching

  22. Bilitchenko L, Liu A, Cheung S, Weeding E, Xia B, Leguia M, Densmore D (2011). Eugene—a domain specific language for specifying and constraining synthetic biological parts, devices, and systems. PLoS One 6(4):e18882. doi: 10.1371/journal.pone.0018882

  23. BioBricks Foundation (2011) Retrieved from http://biobricks.org/

  24. Block F, Horn MS, Phillips BC, Diamond J, Evans EM, Shen C (2012) The DeepTree exhibit: visualizing the tree of life to facilitate informal learning. In: Ming L (ed) IEEE transactions on visualization and computer graphics. IEEE, Atlanta

  25. Brooks FP, Ouh-Young M, Kilpatrick PJ (1990) Project GROPEHaptic displays for scientific visualization. In: Beach RJ (ed) SIGGRAPH computer graphics and interactive techniques. ACM SIGGRAPH, Dallas, pp 177–185

  26. Cai Y, Wilson M, Peccoud J (2012) GenoCAD for iGEM: a grammatical approach to the design of standard-compliant constructs. Nucleic Acids Res 38(8):2637–3644

    Google Scholar 

  27. Carini RK (2006) Student engagement and student learning: testing the linkages. Res High Educ 47(1):1–32

    Google Scholar 

  28. Chandran D, Bergmann F, Sauro H (2009). TinkerCell: modular CAD tool for synthetic biology. J Biol Eng 3:19

    Google Scholar 

  29. Chandrasekharan S (2009) Building to discover: a common coding model. Cogn Sci 33(6):1059–1086

    Article  Google Scholar 

  30. Chang K, Xu W, Francisco N, Valdes C, Kincaid R, Shaer O (2012) SynFlo: an interactive installation introducing synthetic biology concepts. In: Interactive tabletops and surfaces. ACM, Cambridge

  31. Corno LA (1983) The role of cognitive engagement in classroom learning and motivation. Educ Psychol 18(2):88–108

    Google Scholar 

  32. Cox D (1991) Collaborations in art/science: renaissance teams. J Biocommun 18(2):10–15

    Google Scholar 

  33. Davies M, Gould S, Ma S, Mullin V, Stanley M, Walbridge A, Wilson C (2009) E. chromi Cambridge. Retrieved 2011, from Cambridge iGEM Team: http://www.google.com/url?q=http%3A%2F%2F2009.igem.org%2FTeam%3ACambridge&sa=D&sntz=1&usg=AFQjCNF1Fr1mXKhrQk6UiJkJJotF1NzAtQ

  34. Fishkin K (2004) A taxonomy for and analysis of tangible interfaces. Pers Ubiquit Comput 8(5):347–358

    Google Scholar 

  35. Ghamari R, Stanton B, Haddock T, Bhatia S, Clancy K, Peterson T, Densmore D (2011) Applying hardware description languages to genetic circuit design. In: International workshop on bio-design automation

  36. Gillet A, Sanner M, Stoffler D, Goodsell D, Olson A (2004) Augmented reality with tangible auto-fabricated models for molecular biology applications. In: Visualization. IEEE, Austin

  37. Glenberg AM (2008) Embodiment for education. In: Calvo P, Gomila T (ed) Handbook of cognitive science: an embodied approach, pp 355–372

  38. Hart SG, Staveland LE (1988) Development of NASA-TLX (task load index): results of empirical and theoretical research. In: Hancock PA, Meshkati N (eds) Human Mental Workload. North Holland Press, Amsterdam

  39. Hollan J, Hutchins E, Kirsh D (2000). Distributed cognition: toward a new foundation for human-computer interaction research. In: Grudin J (ed) Human factors in computing systems. ACM, Hague, pp 174–196

  40. Horn M, Tobiasz M, Shen C (2009) Visualizing biodiversity with voronoi treemaps. In: Anton F (ed) International symposium on voronoi diagrams in science and engineering. IEEE, Copenhagen, pp 265–270

  41. Hornecker E, Buur J (2006) Getting a grip on tangible interaction: a framework on physical space and social interaction. In: Grinter R, Rodden T, Aoki P, Cutrell E, Jeffries R, Olson G (eds) Human factors in computing systems. ACM, New York, pp 437–446

  42. Jacob RJ, Girouard A, Hirshfield L, Horn MS, Shaer O, Solovey ET, Zigelbaum J (2008) Reality-based interaction: a framework for post-WIMP interfaces. In: Human factors in computing systems. ACM, Florence

  43. Jermann P, Zufferey G, Schneider B, Lucci A, Lepine S, Dillenbourg P (2003). Physical space and division of labor around a tabletop tangible simulation. In: O'Malley C, Suthers D, Reimann P, Dimitracopoulou A (eds) International computer-supported collaborative learning. ISLS, Rhodes, pp 345–349

  44. Keasling JD (2007) Renewable energy from synthetic biology. Retrieved from nanoHUB.org: http://nanohub.org/resources/3297

  45. Kirby JR (2010) Designer bacteria degrades toxin. Nat Chem Biol 6(6):398–399

    Article  Google Scholar 

  46. Kirsh D (1995) The intelligent use of space. Artif Intell 73(1–2):31–68

    Google Scholar 

  47. Kirsh D, Maglio P (1994) On distinguishing epistemic from pragmatic action. Cogn Sci 18(4):513–549

    Google Scholar 

  48. Kuldell N (2007) Authentic teaching through synthetic biology. J Biol Eng 20(2):156–160

    Google Scholar 

  49. Kuznetsov ST (2012) (DIY) biology and opportunities for HCI. In: Designing interactive systems. ACM, Newcastle

  50. Linshiz G, Stawski N, Poust S, Bi C, Keasling JD, Hillson NJ (2012) PaR–PaR laboratory automation platform. ACS Synth Biol 2(5):216–222

  51. Liu S, Lu K, Seifeselassie N, Grote C, Francisco N, Lin V, Shaer O (2012) MoClo Planner: supporting innovation in bio-design through multitouch interaction. In: Interactive tabletops and surfaces. ACM, Cambridge

  52. Marshall P (2007) Do tangible interfaces enhance learning? In: TEI. ACM Press, LA, pp 163–170

  53. Mitchell R, Yehudit JD (2011) Experiential engineering through iGEM—an undergraduate summer competition in synthetic biology. J Sci Educ Technol 20(2):156

    Google Scholar 

  54. Nersessian NJ (2002) The cognitive basis of model-based reasoning in science. In: Carruthers P, Stich S, Siegal M (eds) The cognitive basis of science. Cambridge University Press, Cambridge, pp 133–153

    Chapter  Google Scholar 

  55. Nersessian NJ (2008) Creating scientific concepts. MIT Press, Cambridge

    Google Scholar 

  56. Newstetter W, Behravesh E, Nersessian N, Fasse B (2010) Design principles for problem-driven learning laboratories in biomedical engineering education. Retrieved October 2010, from NCBI: http://www.ncbi.nlm.nih.gov/pubmed/20480239

  57. O’brien HL, Toms E (2008) What is user engagement? A conceptual framework for defining user engagement with technology. J Am Soc Inf Sci Technol 59(6):938–955

    Google Scholar 

  58. Okada T, Simon H (1997) Collaborative discovery in a scientific domain. Cogn Sci 21(2):109–146

    Google Scholar 

  59. Piaget J (1952) The origins of intelligence in children. International Universities Press, New York

    Book  Google Scholar 

  60. Price S, Sheridan J, Falcao T, Roussos G (2008) Towards a framework for investigating tangible environments for learning. Int J Art Technol (special issue on Tangible and Embedded Interaction) 1(3–4):351–368

    Google Scholar 

  61. Rotgans J, Schmidt H (2011) The role of teachers in facilitating situational interest in an active-learning classroom. Teach Teach Educ 27(1):37–42

    Google Scholar 

  62. Rubacha M, Rattan A, Hosselet S (2011) A review of electronic laboratory notebooks available in the market today. J Assoc Lab Autom 16(1):90–98

    Google Scholar 

  63. Ryall K, Morris MR, Everitt K, Forlines C, Shen C (2006) Experiences with and observations of direct-touch tabletops. In: Tabletop. IEEE, Cambridge

  64. Salis H (2011) The ribosome binding site calculator. Methods Enzymol 498:19–42

    Article  Google Scholar 

  65. Scaiffe M, Rogers Y (1996) External cognition: how do graphical representations work? Int J Hum Comput Stud 45(2):185–213

    Google Scholar 

  66. Schindler S (2007) Model, theory, and evidence in the discovery of the DNA structure. HPS1 Integr Hist Philos Sci

  67. Schkolne S, Ishii H, Schroder P (2004) Immersive design of DNA molecules with a tangible interface. In: Visualization. IEEE, Washington, DC, pp 227–234

  68. Schneider BJ (2011) Benefits of a tangible interface for collaborative learning and interaction. IEEE Trans Learn Technol 4(3):222–232

    Google Scholar 

  69. Schneider B, Strait M, Muller L, Elfenbein S, Shaer O, Shen C (2012) Phylo-genie: engaging students in collaborative ‘treethinking’ through tabletop techniques. In: Human factors in computing systems. ACM, Austin

  70. Shaer O, Hornecker E (2010) Tangible user interfaces: past, present, and future directions. Found Trends Hum Comput Interact 3(1–2):1–137

    Google Scholar 

  71. Shaer O, Kol G, Strait M, Fan C, Catherine G, Elfenbein S (2010) G-nome surfer: a tabletop interface for collaborative. In: Conference on human factors in computing systems. ACM

  72. Shaer O, Leland N, Calvillo-Gamez E, Jacob R (2004) The TAC paradigm: specifying tangible user interfaces. Pers Ubiquit Comput 8(5):359–369

    Google Scholar 

  73. Shaer O, Mazalek A, Ullmer B, Konkell M (2013) From big data to insights: opportunities and challenges for TEI in genomics. In: Tangible, embedded and embodied interaction. ACM, Barcelona

  74. Shaer O, Strait M, Valdes C, Feng T, Lintz M, Wang H (2011) Enhancing genomic learning through tabletop interaction. In: Human factors in computing systems. ACM, Vancouver

  75. Shaer O, Strait M, Valdes C, Wang H, Feng T, Lintz M, Liu S (2012) The design, development, and deployment of a tabletop interface for collaborative exploration of genomic data. Int J Hum Comput Stud 70(10):746–764

    Google Scholar 

  76. Synthetic Biology Open Language (2011) Retrieved from http://www.sbolstandard.org/

  77. Tabard A, Hincapie-Ramos JD, Bardram JE (2012) The eLabBench in the wild—supporting exploration in a molecular biology lab. In: Human factors in computing systems. ACM, Austin

  78. Tabard A, Mackay W, Eastmond E (2008) From individual to collaborative: the evolution of prism, a hybrid laboratory notebook. In: Computer supported cooperative work. ACM, New York, pp 569–578

  79. Valdes C, Ferreirae M, Feng T, Wang H, Tempel K, Liu S, Shaer O (2012) A collaborative environment for engaging novices in scientific inquiry. In: Interactice tabletops and surfaces. ACM, Cambridge

  80. Vasilev V, Liu C, Haddock T, Bhatia S, Adler A, Yaman F, Densmore D (2011) A software stack for specification and robotic execution of protocols for synthetic biological engineering. In: Workshop on bio-design automation

  81. Weber E, Engler C, Gruetzner R, Werner S, Marillonnet S (2011) A modular cloning system for standardized assembly of multigene constructs. PLoS One 6(2):e16765

    Google Scholar 

  82. Wigdor D, Jiang H, Forlines C, Borking M, Shen C (2009). The WeSpace: the design, development, and deployment of a walk-up and share multi-surface visual collaboration system. In: Human factors in computing systems. ACM, Boston

  83. Wilson M (2002) Six views of embodied cognition. Psychon Bull Rev 9(4):625–636

    Google Scholar 

  84. Xia B, Bhatia S (2011). Clotho: a software platform for the creation of synthetic biological systems, a developer’s and user’s guide for Clotho v2.0. Methods Enzymol 498:97–135

    Google Scholar 

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Acknowledgments

We thank the students who contributed to this work: Nahum Seifeselassie, Casey Grote, Linda Ding, Nicole Francisco, Veronica Lin, Madeleine Barowsky, and Taili Feng. We also gratefully acknowledge Natalie Kuldell from MIT and Dave Olsen from Wellesley College who provided advice and support. Finally, we thank the Boston University and MIT iGEM teams. This work was partially funded by NSF Grant No. IIS-1149530 and by a grant from Agilent Technologies.

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Correspondence to Orit Shaer.

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Shaer, O., Valdes, C., Liu, S. et al. Designing reality-based interfaces for experiential bio-design. Pers Ubiquit Comput 18, 1515–1532 (2014). https://doi.org/10.1007/s00779-013-0752-1

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