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Tangible BioNets: Multi-Surface and Tangible Interactions for Exploring Structural Features of Biological Networks

Authors:

Roozbeh Manshaei,

Ali MazalekAuthors Info & Claims

Proceedings of the ACM on Human-Computer Interaction, Volume 3, Issue EICS

Article No.: 14, Pages 1 - 22

https://doi.org/10.1145/3331156

Published: 13 June 2019 Publication History

Abstract

Biological networks analysis has become a systematic and large-scale phenomenon. Most biological systems are often difficult to interpret due to the complexity of relationships and structural features. Moreover, existing primarily web-based interfaces for biological networks analysis often have limitations in usability as well as in supporting high-level reasoning and collaboration. Interactive surfaces coupled with tangible interactions offer opportunities to improve the comparison and analysis of large biological networks, which can aid researchers in making hypotheses and forming insights. We present Tangible BioNets, an active tangible and multi-surface system that allows users with diverse expertise to explore and understand the structural and functional aspects of biological organisms individually or collaboratively. The system was designed through an iterative co-design process and facilitates the exploration of biological network topology, catalyzing the generation of new insights. We describe a first informal evaluation with expert users and discuss considerations for designing tangible and multi-surface systems for large biological datasets.

References

[1]

Al-Megren, S., & Ruddle, R. A. (2016, February). Comparing tangible and multi-touch interaction for interactive data visualization tasks. In Proceedings of the TEI'16: Tenth International Conference on Tangible, Embedded, and Embodied Interaction (pp. 279--286). ACM.

Digital Library

[2]

Andrews, C., Endert, A., & North, C. (2010, April). Space to think: large high-resolution displays for sense-making. In Proceedings of the SIGCHI conference on human factors in computing systems (pp. 55--64). ACM.

Digital Library

[3]

Arif, A. S., Manshaei, R., Delong, S., East, B., Kyan, M., & Mazalek, A. (2016, February). Sparse Tangibles: Collaborative exploration of gene networks using active tangibles and interactive tabletops. In Proceedings of the TEI'16: Tenth International Conference on Tangible, Embedded, and Embodied Interaction (pp. 287--295). ACM.

Digital Library

[4]

Ball, R., North, C., & Bowman, D. A. (2007, April). Move to improve: promoting physical navigation to increase user performance with large displays. In Proceedings of the SIGCHI conference on Human factors in computing systems (pp. 191--200). ACM.

Digital Library

[5]

Barabási, A. L. (2016). Network science. Cambridge university press.

Digital Library

[6]

Bi, X., & Balakrishnan, R. (2009, April). Comparing usage of a large high-resolution display to single or dual desktop displays for daily work. In Proceedings of the SIGCHI Conference on Human Factors in Computing Systems (pp. 1005--1014). ACM.

Digital Library

[7]

Bier, E. A., Stone, M. C., Pier, K., Buxton, W., & DeRose, T. D. (1993, September). Toolglass and magic lenses: the see-through interface. In Proceedings of the 20th annual conference on Computer graphics and interactive techniques (pp. 73--80). ACM.

Digital Library

[8]

Card, S. K., Mackinlay, J. D., & Shneiderman, B. (1999). Information visualization: Using vision to think. San Francisco: Morgan Kaufmann Publishers.

Digital Library

[9]

Catalá, A., Garcia-Sanjuan, F., Jaen, J., & Mocholi, J. A. (2012). TangiWheel: a widget for manipulating collections on tabletop displays supporting hybrid input modality. Journal of Computer Science and Technology, 27(4), 811--829.

[10]

Czerwinski, M., Smith, G., Regan, T., Meyers, B., Robertson, G. G., & Starkweather, G. K. (2003). Toward characterizing the productivity benefits of very large displays. In Interact (Vol. 3, pp. 9--16).

[11]

East, B., DeLong, S., Manshaei, R., Arif, A., & Mazalek, A. (2016, November). Actibles: open source active tangibles. In Proceedings of the 2016 ACM on Interactive Surfaces and Spaces (pp. 469--472). ACM.

Digital Library

[12]

Emmert-Streib, F. (2012). Limitations of gene duplication models: Evolution of modules in protein interaction networks. PloS one, 7(4), e35531.

[13]

Grote, C., Segreto, E., Okerlund, J., Kincaid, R., & Shaer, O. (2015, January). Eugenie: Multi-touch and tangible interaction for bio-design. In Proceedings of the Ninth International Conference on Tangible, Embedded, and Embodied Interaction (pp. 217--224). ACM.

Digital Library

[14]

Hearst, M. A. (2014). What's missing from collaborative search? Computer, 47(3), 58--61.

Digital Library

[15]

Holmquist, L.E., Redström, J., & Ljungstrand, P. (1999). Token-based access to digital information. Proc. First Int. Symp. Handheld and Ubiquitous Computing, HUC '99, pp. 234--245. Karlsruhe, Germany: Springer--Verlag.

Digital Library

[16]

Kairam, S., MacLean, D., Savva, M., & Heer, J. (2012, May). GraphPrism: compact visualization of network structure. In Proceedings of the International Working Conference on Advanced Visual Interfaces (pp. 498--505). ACM.

Digital Library

[17]

Kozlikova, B., Krone, M., Lindow, N., Falk, M., Baaden, M., Baum, D., ... & Hege, H. C. (2015, April). Visualization of biomolecular structures: State of the art. In Eurographics Conference on Visualization (EuroVis)-STARs (pp. 061-081). The Eurographics Association.

[18]

Lehner, B. (2011). Molecular mechanisms of epistasis within and between genes. Trends in Genetics, 27(8), 323--331.

[19]

Liu, C., Chapuis, O., Beaudouin-Lafon, M., Lecolinet, E., & Mackay, W. E. (2014, April). Effects of display size and navigation type on a classification task. In Proceedings of the 32nd annual ACM conference on Human factors in computing systems (pp. 4147--4156). ACM.

Digital Library

[20]

Mirel, B. (2009). Supporting cognition in systems biology analysis: findings on users' processes and design implications. Journal of Biomedical discovery and Collaboration, 4(1), 2.

[21]

Okerlund, J., Segreto, E., Grote, C., Westendorf, L., Scholze, A., Littrell, R., & Shaer, O. (2016, February). Synflo: A tangible museum exhibit for exploring bio-design. In Proceedings of the TEI'16: Tenth International Conference on Tangible, Embedded, and Embodied Interaction (pp. 141--149). ACM.

Digital Library

[22]

Pavlopoulos, G. A., Malliarakis, D., Papanikolaou, N., Theodosiou, T., Enright, A. J., & Iliopoulos, I. (2015). Visualizing genome and systems biology: technologies, tools, implementation techniques and trends, past, present and future. Giga Science, 4(1), 38.

[23]

Reda, K., Johnson, A. E., Papka, M. E., & Leigh, J. (2015, April). Effects of display size and resolution on user behavior and insight acquisition in visual exploration. In Proceedings of the 33rd Annual ACM Conference on Human Factors in Computing Systems (pp. 2759--2768). ACM.

Digital Library

[24]

Shaer, O., Mazalek, A., Ullmer, B., & Konkel, M. (2013, February). From big data to insights: opportunities and challenges for TEI in genomics. In Proceedings of the 7th International Conference on Tangible, Embedded and Embodied Interaction (pp. 109--116). ACM.

Digital Library

[25]

Shaer, O., Kol, G., Strait, M., Fan, C., Grevet, C., & Elfenbein, S. (2010, April). G-nome surfer: a tabletop interface for collaborative exploration of genomic data. In Proceedings of the SIGCHI Conference on Human Factors in Computing Systems (pp. 1427--1436). ACM.

Digital Library

[26]

Stark, C., Breitkreutz, B. J., Reguly, T., Boucher, L., Breitkreutz, A., & Tyers, M. (2006). BioGRID: a general repository for interaction datasets. Nucleic acids research, 34(suppl_1), D535-D539.

[27]

Valdes, C., Eastman, D., Grote, C., Thatte, S., Shaer, O., Mazalek, A., ... & Konkel, M. K. (2014, April). Exploring the design space of gestural interaction with active tokens through user-defined gestures. In Proceedings of the SIGCHI Conference on Human Factors in Computing Systems (pp. 4107--4116). ACM.

Digital Library

[28]

Van Steen, K. (2011). Travelling the world of gene--gene interactions. Briefings in bioinformatics, 13(1), 1--19.

[29]

Veretnik, S., Fink, J. L., & Bourne, P. E. (2008). Computational biology resources lack persistence and usability. PLoS computational biology, 4(7), e1000136.

[30]

Yost, B., Haciahmetoglu, Y., & North, C. (2007, April). Beyond visual acuity: the perceptual scalability of information visualizations for large displays. In Proceedings of the SIGCHI conference on Human factors in computing systems (pp. 101--110). ACM.

Digital Library

Cited By

Bakogeorge AImtiaz SAbu Hantash NManshaei RMazalek ACiolfi LHogan TDöring TJenkins Tvan Dijk JHuron SLi ZCoyle DSigner B(2024)Embodied Machine LearningProceedings of the Eighteenth International Conference on Tangible, Embedded, and Embodied Interaction10.1145/3623509.3633370(1-12)Online publication date: 11-Feb-2024
https://dl.acm.org/doi/10.1145/3623509.3633370
Da Costa VZen ETavares T(2023)The interface is on the table: Systematic Literature Review about interaction design to applications for tangible tabletops.Proceedings of the XXII Brazilian Symposium on Human Factors in Computing Systems10.1145/3638067.3638091(1-12)Online publication date: 16-Oct-2023
https://dl.acm.org/doi/10.1145/3638067.3638091
Manshaei RMayat UImtiaz SAndric VAliar KAbu Hantash NMasood KResch GBakogeorge ASabatinos SMazalek A(2022)Tangible Chromatin: Tangible and Multi-surface Interactions for Exploring Datasets from High-Content Microscopy ExperimentsProceedings of the ACM on Human-Computer Interaction10.1145/35677116:ISS(51-72)Online publication date: 14-Nov-2022
https://dl.acm.org/doi/10.1145/3567711
Show More Cited By

Index Terms

Tangible BioNets: Multi-Surface and Tangible Interactions for Exploring Structural Features of Biological Networks
1. Human-centered computing

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Published In

cover image Proceedings of the ACM on Human-Computer Interaction

Proceedings of the ACM on Human-Computer Interaction Volume 3, Issue EICS

June 2019

553 pages

EISSN:2573-0142

DOI:10.1145/3340630

Editors:
Cliff Lampe
University of Michigan
,
Jeff Nichols
Google
,
Karrie Karahalios
University of Illinois Urbana-Champaign
,
Geraldine Fitzpatrick
Vienna University of Technology
,
Uichin Lee
KAIST
,
Andres Monroy-Hernandez
Microsoft Research
,
Wolfgang Stuerzlinger
Simon Fraser University

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Copyright © 2019 ACM.

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Association for Computing Machinery

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Publication History

Published: 13 June 2019

Published in PACMHCI Volume 3, Issue EICS

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Cited By

Bakogeorge AImtiaz SAbu Hantash NManshaei RMazalek ACiolfi LHogan TDöring TJenkins Tvan Dijk JHuron SLi ZCoyle DSigner B(2024)Embodied Machine LearningProceedings of the Eighteenth International Conference on Tangible, Embedded, and Embodied Interaction10.1145/3623509.3633370(1-12)Online publication date: 11-Feb-2024
Da Costa VZen ETavares T(2023)The interface is on the table: Systematic Literature Review about interaction design to applications for tangible tabletops.Proceedings of the XXII Brazilian Symposium on Human Factors in Computing Systems10.1145/3638067.3638091(1-12)Online publication date: 16-Oct-2023
Manshaei RMayat UImtiaz SAndric VAliar KAbu Hantash NMasood KResch GBakogeorge ASabatinos SMazalek A(2022)Tangible Chromatin: Tangible and Multi-surface Interactions for Exploring Datasets from High-Content Microscopy ExperimentsProceedings of the ACM on Human-Computer Interaction10.1145/35677116:ISS(51-72)Online publication date: 14-Nov-2022
Ullmer BShaer OMazalek AHummels C(2022)Weaving Fire into FormundefinedOnline publication date: 20-Jul-2022
Ens BGoodwin SProuzeau AAnderson FWang FGratzl SLucarelli ZMoyle BSmiley JDwyer T(2021)Uplift: A Tangible and Immersive Tabletop System for Casual Collaborative Visual AnalyticsIEEE Transactions on Visualization and Computer Graphics10.1109/TVCG.2020.303033427:2(1193-1203)Online publication date: Feb-2021
Konkel MUllmer BShaer OMazalek ABranton C(2020)Toward tangibles and display-rich interfaces for co-located and distributed genomics collaborationsPersonal and Ubiquitous Computing10.1007/s00779-020-01376-526:3(767-779)Online publication date: 5-Mar-2020

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