We created a visualization tool called Circos to facilitate the identification and analysis of similarities and differences arising from comparisons of genomes. Our tool is effective in displaying variation in genome structure and, generally, any other kind of positional relationships between genomic intervals. Such data are routinely produced by sequence alignments, hybridization arrays, genome mapping, and genotyping studies. Circos uses a circular ideogram layout to facilitate the display of relationships between pairs of positions by the use of ribbons, which encode the position, size, and orientation of related genomic elements. Circos is capable of displaying data as scatter, line, and histogram plots, heat maps, tiles, connectors, and text. Bitmap or vector images can be created from GFF-style data inputs and hierarchical configuration files, which can be easily generated by automated tools, making Circos suitable for rapid deployment in data analysis and reporting pipelines.

/pdf/circos-an-information-aesthetic-for-comparative-genomics-qxy5v3wfu9.pdf

Circos: An information aesthetic for comparative genomics

http://science.sciencemag.org/content/sci/201/4359/899.2.full.pdf

Phenomenology of perception.

Truth and method

This invention relates to customized electronic identification of desirable objects, such as news articles, in an electronic media environment, and in particular to a system that automatically constructs both a "target profile" for each target object in the electronic media based, for example, on the frequency with which each word appears in an article relative to its overall frequency of use in all articles, as well as a "target profile interest summary" for each user, which target profile interest summary describes the user's interest level in various types of target objects. The system then evaluates the target profiles against the users' target profile interest summaries to generate a user-customized rank ordered listing of target objects most likely to be of interest to each user so that the user can select from among these potentially relevant target objects, which were automatically selected by this system from the plethora of target objects that are profiled on the electronic media. Users' target profile interest summaries can be used to efficiently organize the distribution of information in a large scale system consisting of many users interconnected by means of a communication network. Additionally, a cryptographically-based pseudonym proxy server is provided to ensure the privacy of a user's target profile interest summary, by giving the user control over the ability of third parties to access this summary and to identify or contact the user.

System for generation of user profiles for a system for customized electronic identification of desirable objects

Mobile devices are becoming increasingly sophisticated and the latest generation of smart cell phones now incorporates many diverse and powerful sensors These sensors include GPS sensors, vision sensors (ie, cameras), audio sensors (ie, microphones), light sensors, temperature sensors, direction sensors (ie, magnetic compasses), and acceleration sensors (ie, accelerometers) The availability of these sensors in mass-marketed communication devices creates exciting new opportunities for data mining and data mining applications In this paper we describe and evaluate a system that uses phone-based accelerometers to perform activity recognition, a task which involves identifying the physical activity a user is performing To implement our system we collected labeled accelerometer data from twenty-nine users as they performed daily activities such as walking, jogging, climbing stairs, sitting, and standing, and then aggregated this time series data into examples that summarize the user activity over 10- second intervals We then used the resulting training data to induce a predictive model for activity recognition This work is significant because the activity recognition model permits us to gain useful knowledge about the habits of millions of users passively---just by having them carry cell phones in their pockets Our work has a wide range of applications, including automatic customization of the mobile device's behavior based upon a user's activity (eg, sending calls directly to voicemail if a user is jogging) and generating a daily/weekly activity profile to determine if a user (perhaps an obese child) is performing a healthy amount of exercise

/pdf/activity-recognition-using-cell-phone-accelerometers-3k6h9fhibm.pdf

Activity recognition using cell phone accelerometers

This paper characterises the use of activity trackers as "lived informatics". This characterisation is contrasted with other discussions of personal informatics and the quantified self. The paper reports an interview study with activity tracker users. The study found: people do not logically organise, but interweave various activity trackers, sometimes with ostensibly the same functionality; that tracking is often social and collaborative rather than personal; that there are different styles of tracking, including goal driven tracking and documentary tracking; and that tracking information is often used and interpreted with reference to daily or short term goals and decision making. We suggest there will be difficulties in personal informatics if we ignore the way that personal tracking is enmeshed with everyday life and people's outlook on their future.

/pdf/personal-tracking-as-lived-informatics-15jozgp8li.pdf

Personal tracking as lived informatics

While tourism presents considerable potential for the use of new mobile technologies, we currently have little understanding of how tourists organise their activities or of the problems they face. This paper presents an ethnographic study of city tourists' practices that draws out a number of implications for designing tourist technology. We describe how tourists work together in groups, collaborate around maps and guidebooks, and both 'pre-' and 'post-visit' places. Implications are drawn for three types of tourist technology: systems that explicitly support how tourists co-ordinate, electronic guidebooks and maps, and electronic tour guide applications. We discuss applications of these findings, including the Travelblog, which supports building travel-based web pages while on holiday.

/pdf/tourism-and-mobile-technology-56368nlxid.pdf

Tourism and mobile technology

Design experience and theoretical discussion suggest that a narrow design focus on one tool or medium as primary may clash with the way that everyday activity involves the interweaving and combination of many heterogeneous media. Interaction may become seamless and unproblematic, even if the differences, boundaries and 'seams' in media are objectively perceivable. People accommodate and take advantage of seams and heterogeneity, in and through the process of interaction. We use an experiment with a mixed reality system to ground and detail our discussion of seamful design, which takes account of this process, and theory that reflects and informs such design. We critique the 'disappearance' mentioned by Weiser as a goal for ubicomp, and Dourish's 'embodied interaction' approach to HCI, suggesting that these design ideals may be unachievable or incomplete because they underemphasise the interdependence of 'invisible' non-rationalising interaction and focused rationalising interaction within ongoing activity.

/pdf/seamful-interweaving-heterogeneity-in-the-theory-and-design-v1lrf7vqcc.pdf

Seamful interweaving: heterogeneity in the theory and design of interactive systems

We introduce a location--based game called Feeding Yoshi that provides an example of seamful design, in which key characteristics of its underlying technologies-the coverage and security characteristics of WiFi-are exposed as a core element of gameplay. Feeding Yoshi is also a long--term, wide--area game, being played over a week between three different cities during an initial user study. The study, drawing on participant diaries and interviews, supported by observation and analysis of system logs, reveals players' reactions to the game. We see the different ways in which they embedded play into the patterns of their daily lives, augmenting existing practices and creating new ones, and observe the impact of varying location on both the ease and feel of play. We identify potential design extensions to Feeding Yoshi and conclude that seamful design provides a route to creating engaging experiences that are well adapted to their underlying technologies.

/pdf/interweaving-mobile-games-with-everyday-life-2aebc7rxo4.pdf

Interweaving mobile games with everyday life

We describe work on the visualization of bibliographic data and, to aid in this task, the application of numerical techniques for multidimensional scaling.Many areas of scientific research involve complex multivariate data. One example of this is Information Retrieval. Document comparisons may be done using a large number of variables. Such conditions do not favour the more well-known methods of visualization and graphical analysis, as it is rarely feasible to map each variable onto one aspect of even a three-dimensional, coloured and textured space.Bead is a prototype system for the graphically-based exploration of information. In this system, articles in a bibliography are represented by particles in 3-space. By using physically-based modelling techniques to take advantage of fast methods for the approximation of potential fields, we represent the relationships between articles by their relative spatial positions. Inter-particle forces tend to make similar articles move closer to one another and dissimilar ones move apart. The result is a 3D scene which can be used to visualize patterns in the high-D information space.

/pdf/bead-explorations-in-information-visualization-3zfcx2cuyh.pdf

Matthew Chalmers

Papers

Personal tracking as lived informatics

Tourism and mobile technology

Seamful interweaving: heterogeneity in the theory and design of interactive systems

Interweaving mobile games with everyday life

Bead: explorations in information visualization