Ahmed Sabbir Arif
Roozbeh Manshaei
ABSTRACT
We present Sparse Tangibles, a tabletop and active tangible-based framework to support cross-platform, collaborative gene network exploration using a Web interface. It uses smartwatches as active tangibles to allow query construction on- and off-the-table. We expand their interaction vocabulary using inertial sensors and a custom case. We also introduce a new metric for measuring the "confidence level" of protein and genetic interactions. Three expert biologists evaluated the system and found it fun, useful, easy to use, and ideal for collaborative explorations.
- Albert-László Barabási. 2015. Network Science. Cambridge University. Retrieved July 21, 2015 from http://www.barabasi.com/networksciencebookGoogle Scholar
- Andreas Beyer, Sourav Bandyopadhyay, and Trey Ideker. 2007. Integrating physical and genetic maps: From genomes to interaction networks. Nature Reviews Genetics 8, 9: 699--710.Google ScholarCross Ref
- Kevin R. Brown, David Otasek, Muhammad Ali, Michael J. McGuffin, Wing Xie, Baiju Devani, Ian Lawson van Toch, and Igor Jurisica. 2009. NAViGaTOR: network analysis, visualization and graphing Toronto. Bioinformatics 25, 24: 3327--3329. Google ScholarDigital Library
- Ken Camarata, Ellen Yi-Luen Do, Brian R. Johnson, and Mark D. Gross. 2002. Navigational blocks: navigating information space with tangible media. In Proceedings of the 7th international conference on Intelligent user interfaces (IUI '02). ACM, New York, NY, USA, 31--38. Google ScholarDigital Library
- Andrew Chatr-aryamontri, Bobby-Joe Breitkreutz, Rose Oughtred, Lorrie Boucher, Sven Heinicke, Daici Chen, Chris Stark, Ashton Breitkreutz, Nadine Kolas, Lara O'Donnell, Teresa Reguly, Julie Nixon, Lindsay Ramage, Andrew Winter, Adnane Sellam, Christie Chang, Jodi Hirschman, Chandra Theesfeld, Jennifer Rust, Michael S. Livstone, Kara Dolinski, and Mike Tyers. 2014. The BioGRID interaction database: 2015 update. Nucleic Acids Research: gku1204.Google Scholar
- Zhenjun Hu, Joe Mellor, Jie Wu, Takuji Yamada, Dustin Holloway, and Charles DeLisi. 2005. VisANT: data-integrating visual framework for biological networks and modules. Nucleic Acids Research 33, 2: W352-W357.Google ScholarCross Ref
- Hans-Christian Jetter, Jens Gerken, Michael Zöllner, Harald Reiterer, and Natasa Milic-Frayling. 2011. Materializing the query with facet-streams: a hybrid surface for collaborative search on tabletops. In Proceedings of the SIGCHI Conference on Human Factors in Computing Systems (CHI '11). ACM, New York, NY, USA, 3013--3022. Google ScholarDigital Library
- Stefanie Klum, Petra Isenberg, Ricardo Langner, Jean-Daniel Fekete, and Raimund Dachselt. 2012. Stackables: combining tangibles for faceted browsing. In Proceedings of the International Working Conference on Advanced Visual Interfaces (AVI '12), Genny Tortora, Stefano Levialdi, and Maurizio Tucci (Eds.). ACM, New York, NY, USA, 241--248. Google ScholarDigital Library
- Christina Laufer, Bernd Fischer, Wolfgang Huber, and Michael Boutros. 2014. Measuring genetic interactions in human cells by RNAi and imaging. Nature Protocols 9, 10: 2341--2353.Google ScholarCross Ref
- Robert D. Leclerc. 2008. Survival of the sparsest: robust gene networks are parsimonious. Molecular Systems Biology 4, 1: 213.Google ScholarCross Ref
- Ben Lehner. 2011. Molecular mechanisms of epistasis within and between genes. Trends in Genetics 27, 8: 323--331.Google ScholarCross Ref
- Martin Kaltenbrunner and Ross Bencina. 2007. reacTIVision: a computer-vision framework for table-based tangible interaction. In Proceedings of the 1st international conference on Tangible and embedded interaction (TEI '07). ACM, New York, NY, USA, 69--74. Google ScholarDigital Library
- Ali Mazalek and Ahmed Sabbir Arif. 2014. Mobile-based tangible interaction techniques for shared displays. In Proceedings of the 16th international conference on Human-computer interaction with mobile devices & services (MobileHCI '14). ACM, New York, NY, USA, 561--562. Google ScholarDigital Library
- Vishal R. Patel, K. Eckel-Mahan, P. Sassone-Corsi, and P. Baldi. 2014. How pervasive are circadian oscillations? Trends in Cell Biology 24, 6: 329--331.Google ScholarCross Ref
- Patrick C. Phillips. 2008. Epistasis---the essential role of gene interactions in the structure and evolution of genetic systems. Nature Reviews Genetics 9, 11: 855--867.Google ScholarCross Ref
- Jun Rekimoto, Brygg Ullmer, and Haruo Oba. 2001. DataTiles: a modular platform for mixed physical and graphical interactions. In Proceedings of the SIGCHI Conference on Human Factors in Computing Systems (CHI '01). ACM, New York, NY, USA, 269--276. Google ScholarDigital Library
- Steven Schkolne, Hiroshi Ishii, and Peter Schroder. 2004. Immersive Design of DNA Molecules with a Tangible Interface. In Proceedings of the conference on Visualization '04 (VIS '04). IEEE Computer Society, Washington, DC, USA, 227--234. Google ScholarDigital Library
- Orit Shaer, Megan Strait, Consuelo Valdes, Heidi Wang, Taili Feng, Michael Lintz, Michelle Ferreirae, Casey Grote, Kelsey Tempel, and Sirui Liu. 2012. The design, development, and deployment of a tabletop interface for collaborative exploration of genomic data. International Journal of Human-Computer Studies 70, 10: 746--764. Google ScholarDigital Library
- Paul Shannon, Andrew Markiel, Owen Ozier, Nitin S. Baliga, Jonathan T. Wang, Daniel Ramage, Nada Amin, Benno Schwikowski, and Trey Ideker. 2003. Cytoscape: a software environment for integrated models of biomolecular interaction networks. Genome Research 13, 11: 2498--2504.Google ScholarCross Ref
- Brygg Ullmer, Hiroshi Ishii, and Robert J. K. Jacob. 2003. Tangible query interfaces: physically constrained tokens for manipulating database queries. In Proceedings of the International Conference on Human-Computer Interaction (INTERACT '03), Vol. 3. IOS, Amsterdam, the Netherlands, 279--286.Google Scholar
- Consuelo Valdes, Diana Eastman, Casey Grote, Shantanu Thatte, Orit Shaer, Ali Mazalek, Brygg Ullmer, and Miriam K. Konkel. 2014. 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 (CHI '14). ACM, New York, NY, USA, 4107--4116. Google ScholarDigital Library
- Kristel Van Steen. Travelling the world of gene--gene interactions. 2011. Briefings in bioinformatics: bbr012.Google Scholar
- David Warde-Farley, Sylva L. Donaldson, Ovi Comes, Khalid Zuberi, Rashad Badrawi, Pauline Chao, Max Franz, Chris Grouios, Farzana Kazi, Christian Tannus Lopes, Anson Maitland, Sara Mostafavi, Jason Montojo, Quentin Shao, George Wright, Gary D. Bader, and Quaid Morris. 2010. The GeneMANIA prediction server: biological network integration for gene prioritization and predicting gene function. Nucleic Acids Research 38, 2: W214-W220.Google ScholarCross Ref
- Yubao Wu, Xiaofeng Zhu, Jian Chen, and Xiang Zhang. 2013. EINVis: a visualization tool for analyzing and exploring genetic interactions in large-scale association studies. Genetic Epidemiology 37, 7: 675--685.Google ScholarCross Ref
- Wendy Xu, Kimberly Chang, Nicole Francisco, Consuelo Valdes, Robert Kincaid, and Orit Shaer. 2013. From wet lab bench to tangible virtual experiment: SynFlo. In Proceedings of the 7th International Conference on Tangible, Embedded and Embodied Interaction (TEI '13). ACM, New York, NY, USA, 399--400. Google ScholarDigital Library
Index Terms
- Sparse Tangibles: Collaborative Exploration of Gene Networks using Active Tangibles and Interactive Tabletops
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