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

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.

[1]  H. Schweingruber,et al.  America's lab report : investigations in high school science , 2006 .

[2]  Nancy J. Nersessian,et al.  Kinesthetic pathways: a tabletop visualization to support discovery in systems biology , 2011, C&C '11.

[3]  David J. DeWitt,et al.  Scientific data management in the coming decade , 2005, SGMD.

[4]  Hiroshi Ishii,et al.  Strata/ICC: physical models as computational interfaces , 2001, CHI Extended Abstracts.

[5]  Brygg Ullmer,et al.  Entangling space, form, light, time, computational STEAM, and cultural artifacts , 2012, INTR.

[6]  Orit Shaer,et al.  The design, development, and deployment of a tabletop interface for collaborative exploration of genomic data , 2012, Int. J. Hum. Comput. Stud..

[7]  Philip E. Bourne,et al.  Computational Biology Resources Lack Persistence and Usability , 2008, PLoS Comput. Biol..

[8]  Vito Perrone,et al.  Better bioinformatics through usability analysis , 2009, Bioinform..

[9]  Yvonne Rogers,et al.  Collaboration and interference: awareness with mice or touch input , 2008, CSCW.

[10]  Orit Shaer,et al.  G-nome surfer: a tabletop interface for collaborative exploration of genomic data , 2010, CHI.

[11]  E. Mardis.  The impact of next-generation sequencing technology on genetics. , 2008, Trends in genetics : TIG.

[12]  Jakob E. Bardram,et al.  The eLabBench: an interactive tabletop system for the biology laboratory , 2011, ITS '11.

[13]  Morten Fjeld,et al.  Tangible user interface for chemistry education: comparative evaluation and re-design , 2007, CHI.

[14]  Orit Shaer,et al.  Enhancing genomic learning through tabletop interaction , 2011, CHI.

[15]  J DeWittDavid,et al.  Scientific data management in the coming decade , 2005 .

[16]  Michael S. Horn,et al.  Visualizing Biodiversity with Voronoi Treemaps , 2009, 2009 Sixth International Symposium on Voronoi Diagrams.

[17]  Hiroshi Ishii,et al.  Immersive design of DMA molecules with a tangible interface , 2004, IEEE Visualization 2004.

[18]  Gaetano Borriello,et al.  Labscape: A Smart Environment for the Cell Biology Laboratory , 2002, IEEE Pervasive Comput..

[19]  Frederick P. Brooks,et al.  Project GROPE-HapticDisplays for Scientific Visualization , 1990 .

[20]  Michael L. Anderson.  Embodied Cognition: A field guide , 2003, Artif. Intell..

[21]  N. Nersessian.  The Cognitive Basis of Science: The cognitive basis of model-based reasoning in science , 2002 .

[22]  Yvonne Rogers,et al.  When the fingers do the talking: A study of group participation with varying constraints to a tabletop interface , 2008, 2008 3rd IEEE International Workshop on Horizontal Interactive Human Computer Systems.

[23]  Albrecht Schmidt,et al.  TEI goes on: Tangible and Embedded Interaction. , 2008 .

[24]  Herbert A. Simon,et al.  Collaborative Discovery in a Scientific Domain , 1997, Cogn. Sci..

[25]  Scott R. Klemmer,et al.  ButterflyNet: a mobile capture and access system for field biology research , 2006, CHI.

[26]  Michel F. Sanner,et al.  Tangible augmented interfaces for structural molecular biology , 2005, IEEE Computer Graphics and Applications.

[27]  Michael Fisher,et al.  Biology Is Technology , 2010 .

[28]  Wendy E. Mackay,et al.  From individual to collaborative: the evolution of prism, a hybrid laboratory notebook , 2008, CSCW.

[29]  L. Chin,et al.  Making sense of cancer genomic data. , 2011, Genes & development.

[30]  Carman Neustaedter,et al.  VideoArms: Embodiments for Mixed Presence Groupware , 2007 .

[31]  Nancy J. Nersessian,et al.  Creating Scientific Concepts , 2008 .

[32]  Albert J. Vilella,et al.  Comparative and demographic analysis of orang-utan genomes , 2011, Nature.

[33]  Chris North,et al.  An insight-based methodology for evaluating bioinformatics visualizations , 2005, IEEE Transactions on Visualization and Computer Graphics.

[34]  Wendy E. Mackay,et al.  The missing link: augmenting biology laboratory notebooks , 2002, UIST '02.

[35]  Jerry Wellington,et al.  America's lab report: Investigations in high school science , 2007 .

[36]  Hao Jiang,et al.  WeSpace: the design development and deployment of a walk-up and share multi-surface visual collaboration system , 2009, CHI.

[37]  Philip Tuddenham,et al.  Distributed Tabletops: Supporting Remote and Mixed-Presence Tabletop Collaboration , 2007, Second Annual IEEE International Workshop on Horizontal Interactive Human-Computer Systems (TABLETOP'07).

[38]  S. Stich,et al.  The cognitive basis of science , 2002 .

[39]  Hiroshi Ishii,et al.  A comparison of spatial organization strategies in graphical and tangible user interfaces , 2000, DARE '00.

[40]  Bertrand Schneider,et al.  Phylo-Genie: engaging students in collaborative 'tree-thinking' through tabletop techniques , 2012, CHI.

[41]  Alex S. Taylor,et al.  (DIY)biology and opportunities for HCI , 2012, DIS '12.

[42]  Bernard McKenna,et al.  Information Arts: Intersections of Art, Science and Technology , 2004 .

[43]  B. Rittle-Johnson,et al.  Does comparing solution methods facilitate conceptual and procedural knowledge? An experimental study on learning to solve equations. , 2007 .

[44]  I. Dubchak,et al.  Visualizing genomes: techniques and challenges , 2010, Nature Methods.

[45]  Meredith Ringel Morris,et al.  Experiences with and observations of direct-touch tabletops , 2006, First IEEE International Workshop on Horizontal Interactive Human-Computer Systems (TABLETOP '06).

[46]  Margaret Wilson,et al.  Six views of embodied cognition , 2002, Psychonomic bulletin & review.

[47]  Barbara Mirel,et al.  Supporting cognition in systems biology analysis: findings on users' processes and design implications , 2009, Journal of biomedical discovery and collaboration.

[48]  Regan L. Mandryk,et al.  System Guidelines for Co-located, Collaborative Work on a Tabletop Display , 2003, ECSCW.