Demos and Posters TEI 2016, February 14-17, 2016, Eindhoven, the Netherlands Sparse Tangibles: Collaborative Exploration of Gene Networks using Active Tangibles and Interactive Tabletops Ahmed Sabbir Arif1, Roozbeh Manshaei1, Sean Delong1, Brien East1, Matthew Kyan3, Ali Mazalek1,2 Synaesthetic Media Laboratory Electrical Engineering & Computer Science3 Ryerson University1 Georgia Institute of York University Toronto, Ontario Technology2 Toronto, Ontario Canada Atlanta, GA, USA Canada {asariF, roozbeh.manshaei, sean.delong, beast, mazalek}@ryerson.ca, [email protected] ABSTRACT fail to work with big data sets or fail to provide the support We present Sparse Tangibles, a tabletop and active tangible- for custom query construction. Most of these solutions are based framework to support cross-platForm, collaborative also system-dependent (that is, do not work with all gene network exploration using a Web interFace. It uses operating systems), require the installation of proprietary smartwatches as active tangibles to allow query construction soFtware, or demand high processing power. Furthermore, on- and oFF-the-table. We expand their interaction vocabulary almost all present solutions are desktop-based, which using inertial sensors and a custom case. We also introduce hinders collaborative exploration and generally limits the a new metric for measuring the “conFidence level” of protein users to smaller screens. and genetic interactions. Three expert biologists evaluated the system and Found it fun, useFul, easy to use, and ideal for We Formed an interdisciplinary team oF six to address these collaborative explorations. issues. Apart From two HCI researchers and an engineer, the group consists oF three expert biomedical/signal processing Author Keywords engineers, whom we identiFy as potential users oF the Systems biology; biomedical engineering; sparse network; system. ThereFore, and to fully utilize their expertise, we visualization; tabletop; active tangibles; participatory design. adopted an iterative design process where all design decisions ACM Classification Keywords were evaluated and analyzed by the team members, and H.5.2 InFormation InterFaces and Presentation (e.g., HCI): interactions were redesigned until every member Found them User InterFaces—input devices and strategies, interaction satisFactory. styles, user-centered design; I.6.7 Simulation and Modeling: Here, we present the Final design oF a novel tabletop-active Simulation Support Systems—environments. tangible-based Framework that supports cross-platForm and INTRODUCTION collaborative gene network exploration using Web interFaces. Gene network exploration is an integral part oF uncovering The intention was not only to design and develop an easy to the secrets and structure of genetic pathways. Biologists use gene network exploration interFace but also to provide explore gene networks to Find the genetic diFFerences and the biology community with a Flexible Framework that can structural evolution among divergent organisms, and to be used to add new visualizations and Features. The intention identiFy the structural limitations on the possible paths oF was also to encourage collaborative exploration and support evolution. Because gene interaction structure is sparse, the non-experts who are coming into an expert domain. structural Features oF a gene interaction network are often The contribution oF our work is threeFold. First, we discuss generalizable across diFFerent organisms. As a result, gene the design and development of a new approach For visualizing exploration oFten points towards “probable” interactions, and manipulating gene networks that can aid in conceptual which results in new discoveries. understanding in both learning and discovery contexts. Currently there is no eFFicient gene interaction network Second, we demonstrate how smartwatches can be used as exploration interFace available. Most present systems either active tangibles on tabletops. We allow users to construct custom queries using smartwatches by expanding their Permission to make digital or hard copies oF all or part oF this work For interaction vocabulary using the inertial sensors and a personal or classroom use is granted without Fee provided that copies are custom case. Finally, we introduce a new method For not made or distributed for profit or commercial advantage and that copies bear this notice and the Full citation on the First page. Copyrights For measuring the conFidence level oF protein and genetic components oF this work owned by others than ACM must be honored. interactions, based on the total number oF articles conFirming Abstracting with credit is permitted. To copy otherwise, or republish, to the interactions and the impact Factor oF the venues that post on servers or to redistribute to lists, requires prior speciFic permission published the articles. and/or a fee. Request permissions from [email protected]. TEI '16, February 14-17, 2016, Eindhoven, Netherlands THE EXPLORATION OF GENE INTERACTIONS © 2016 ACM. ISBN 978-1-4503-3582-9/16/02 ...$15.00 Gene interactions in diFFerent organisms provide an insight DOI: http://dx.doi.org/10.1145/2839462.2839500 into Functional and structural connections among genes and 287 Demos and Posters TEI 2016, February 14-17, 2016, Eindhoven, the Netherlands their produced proteins [11, 22]. The expression of a gene with and understanding of biological concepts and data. For can be either self-regulating or influenced by a collaboration example, Schkolne et al. [17] developed an immersive between itself and other expressing genes. tangible interface for designing DNA components, and SynFlo exploits tangible interaction in combination with a Recently, uncovering the networks of gene interactions (i.e. tabletop to introduce synthetic biology concepts to non- regulatory relationships between genes) has become a experts [25]. Neither system, however, focuses on search or systematic and large-scale phenomenon [9]. Yet, the task of comparison of large data sets. The G-nome Surfer is a analyzing gene interactions is challenging due to the large tabletop multi-touch application for collaborative exploration number of genes, which increases the search space for possible of genomic databases [18]. However, its expressivity is interactions. In addition, the complexity and scale of such limited, as it does not allow users to define and set query networks, either known or inferred, renders the task of operators directly. surveying functional attributes and understanding biological processes within model organisms a challenge in and of itself. Some projects have aimed at the visualization of biological pathways using traditional GUIs. VisANT [6], a Web-based The area of network science has addressed this issue by system, provides a framework for visualizing and analyzing defining gene networks as a set of nodes (e.g. genes or their different types of networks of biological interactions and produced proteins) and edges forming linkages between associations, while Cytoscape supports the visualization and them (e.g. interactions). This simplification makes it easier integration of molecular interaction networks and biological for practitioners to extract local and global structural features pathways [19]. NAViGaTOR [3] is a software package for and provides a better understanding of the processes driving visualizing and analyzing protein-protein interaction the growth and response of living organisms [1]. networks. It can query in two interaction databases and An interaction could be either physical or genetic. A physical display networks in both 2D and 3D. Likewise, EINVis interaction refers to the experience where a direct physical supports the visualization and exploration of the interaction association between two gene products (proteins) has been networks [24], but can only work with smaller networks. identified, while a genetic interaction is identified when the GeneMANIA, in contrast, can find genes that are related to effect of mutating one gene is reflected by the perturbation a set of input genes using a very large set of functional in another gene [2]. Interactions can also be classified as association data [23]. None of these packages, however, inhibitory and excitatory. In an excitatory interaction, the support collaborative exploration. expression of one gene increases/decreases the expression of Our system, in contrast, not only allows users access to large another gene, while in inhibitory interaction, an increase in data sets but also supports collaborative exploration of the the expression of a gene decreases the expression of another data. It also enables users to define and set query operators. gene [14]. Every gene in a regulatory network has one or more activator or inhibitor genes. Thus, to understand the Query Construction using Tangibles structure of a gene interaction network, practitioners usually Numerous tangible interface systems have explored the use explore the network to discover the activators and inhibitors of tangibles for constructing queries. Facet-Streams [7], for of the genes involved. example, allows users to construct expressive queries using passive tangibles on a tabletop display surface. Although, The knowledge of gene interactions also plays an important this system can simplify the construction of complex role in uncovering the structure of genetic pathways. It queries, it has some limitations, including physical clutter, assists researchers and practitioners to better understand the separation of