MOTIVATION: RNA-Seq is a method for profiling transcription using high-throughput sequencing and is an important component of many research projects that wish to study transcript isoforms, condition specific expression and transcriptional structure. The methods, tools and technologies used to perform RNA-Seq analysis continue to change, creating a bioinformatics challenge for researchers who wish to exploit these data. Resources that bring together genomic data, analysis tools, educational material and computational infrastructure can minimize the overhead required of life science researchers. RESULTS: RNA-Rocket is a free service that provides access to RNA-Seq and ChIP-Seq analysis tools for studying infectious diseases. The site makes available thousands of pre-indexed genomes, their annotations and the ability to stream results to the bioinformatics resources VectorBase, EuPathDB and PATRIC. The site also provides a combination of experimental data and metadata, examples of pre-computed analysis, step-by-step guides and a user interface designed to enable both novice and experienced users of RNA-Seq data. AVAILABILITY AND IMPLEMENTATION: RNA-Rocket is available at rnaseq.pathogenportal.org. Source code for this project can be found at github.com/cidvbi/PathogenPortal. CONTACT: [email protected] SUPPLEMENTARY INFORMATION: Supplementary materials are available at Bioinformatics online.

A challenge in presenting augmenting information in outdoor augmented reality (AR) settings lies in the broad range of uncontrollable environmental conditions that may be present, specifically large-scale fluctuations in natural lighting and wide variations in likely backgrounds or objects in the scene. In this paper, we present a active AR testbed that samples the user's field of view, and collects outdoor illuminance values at the participant's position. The main contribution presented herein is a user-based study (conducted using the testbed) that examined the effects on user performance of four outdoor background textures, four text colors, three text drawing styles, and two text drawing style algorithms for a text identification task using an optical, see-through AR system. We report significant effects for all these variables, and discuss design guidelines and ideas for future work

A fundamental problem in optical, see-through augmented reality (AR) is characterizing how it affects the perception of spatial layout and depth. This problem is important because AR system developers need to both place graphics in arbitrary spatial relationships with real-world objects, and to know that users will perceive them in the same relationships. Furthermore, AR makes possible enhanced perceptual techniques that have no real-world equivalent, such as x-ray vision, where AR users are supposed to perceive graphics as being located behind opaque surfaces. This paper reviews and discusses techniques for measuring egocentric depth judgments in both virtual and augmented environments. It then describes a perceptual matching task and experimental design for measuring egocentric AR depth judgments at medium- and far-field distances of 5 to 45 meters. The experiment studied the effect of field of view, the x-ray vision condition, multiple distances, and practice on the task. The paper relates some of the findings to the well-known problem of depth underestimation in virtual environments, and further reports evidence for a switch in bias, from underestimating to overestimating the distance of AR-presented graphics, at 23 meters. It also gives a quantification of how much more difficult the x-ray vision condition makes the task, and then concludes with ideas for improving the experimental methodology.

A challenge in presenting augmenting information in outdoor augmented reality (AR) settings lies in the broad range of uncontrollable environmental conditions that may be present, specifically large-scale fluctuations in natural lighting and wide variations in likely backgrounds or objects in the scene. In this paper, we present a user-based study which examined the effects of outdoor background textures, changing outdoor illuminance values, and text drawing styles on user performance of a text identification task with an optical, see-through augmented reality system. We report significant effects for all of these variables, and discuss design guidelines and ideas for future work.

Provides an abstract of the tutorial presentation and a brief professional biography of the presenter. The complete presentation was not made available for publication as part of the conference proceedings.

A useful function of augmented reality (AR) systems is their ability to visualize occluded infrastructure directly in a user's view of the environment. This is especially important for our application context, which utilizes mobile AR for navigation and other operations in an urban environment. A key problem in the AR field is how to best depict occluded objects in such a way that the viewer can correctly infer the depth relationships between different physical and virtual objects. Showing a single occluded object with no depth context presents an ambiguous picture to the user. But showing all occluded objects in the environments leads to the "Superman's X-ray vision" problem, in which the user sees too much information to make sense of the depth relationships of objects. Our efforts differ qualitatively from previous work in AR occlusion, because our application domain involves far-field occluded objects, which are tens of meters distant from the user. Previous work has focused on near-field occluded objects, which are within or just beyond arm's reach, and which use different perceptual cues. We designed and evaluated a number of sets of display attributes. We then conducted a user study to determine which representations best express occlusion relationships among far-field objects. We identify a drawing style and opacity settings that enable the user to accurately interpret three layers of occluded objects, even in the absence of perspective constraints.

We present a comparative study of user performance with tasks involving navigation, visual search, and geometric manipulation, in a map-based battlefield visualization virtual environment (VE). Specifically, our experiment compared user performance of the same task across four different VE platforms: desktop, cave, workbench, and wall. Independent variables were platform type, stereopsis (stereo, mono), movement control mode (rate, position), and frame of reference (egocentric, exocentric). Overall results showed that users performed tasks fastest using the desktop and slowest using the workbench. Other results are detailed in the article. Notable is that we designed our task in an application context, with tasking much closer to how users would actually use a real-world battlefield visualization system. This is very uncommon for comparative studies, which are usually designed with abstract tasks to minimize variance. This is, we believe, one of the first and most complex studies to comparatively examine, in an application context, this many key variables affecting VE user interface design.

Virtual Reality (VR), Augmented Reality (AR) and other realities along the Mixed Reality(MR) continuum use multi-sensory displays and spatial interaction to enable a number of usefuland novel applications. These virtual worlds are able to train, explore and entertain in addition toaugment the real world with information for our everyday lives. To perform tasks such as traveland other interaction, researchers in these worlds have focused heavily on issues of three-dimensionalinteraction, including interaction techniques, user interface metaphors and inputdevices but always with an outlook centric to their particular position along the MR continuum.This has resulted in interfaces tuned to certain MR instances that are not possible in them allbecause of factors such as the display types, tracking issues or interference and limits from thereal world.This panel brings together diverse researchers across the MR continuum to discuss theirresearch and dissect the similarities and differences of each other's fields. The result is anunderstanding of interfaces across these realities and a merger of developing terminology,techniques and tools for future collaborations.Panel members will give a description of their research followed by a short vision of futureinterface research. Audience questions submitted via index cards are heavily encouraged andexpected to shape the panel discussion and direction.

Social data mining systemsenable people to share opinions and benefit from each other's experience. They do this by mining and redistributing information from computational records of social activity such as Usenet messages, system usage history, citations, or hyperlinks. Some general questions for evaluating such systems are: (1) is the extracted information valuable? and (2) do interfaces based on the information improve user task performance? We report here onTopicShop, a system that mines information from the structure and content of Web pages and provides an exploratory information workspace interface. We carried out experiments that yielded positive answers to both evaluation questions. First, a number of automatically computable features about Web sites do a good job of predicting expert quality judgments about sites. Second, compared to popular Web search interfaces, the TopicShop interface to this information lets users select significantly more high-quality sites, in less time and with less effort, and to organize the sites they select into personally meaningful collections more quickly and easily. We conclude by discussing how our results may be applied and considering how they touch on general issues concerning quality, expertise, and consensus.

Article TopicShop: enhanced support for evaluating and organizing collections of Web sites Share on Authors: Brian Amento AT&T Labs - Research, 180 Park Avenue, P.O. Box 971, Florham Park, NJ and Department of Computer Science, Virginia Tech, Blacksburg, VA AT&T Labs - Research, 180 Park Avenue, P.O. Box 971, Florham Park, NJ and Department of Computer Science, Virginia Tech, Blacksburg, VAView Profile , Loren Terveen AT&T Labs - Research, 180 Park Avenue, P.O. Box 971, Florham Park, NJ AT&T Labs - Research, 180 Park Avenue, P.O. Box 971, Florham Park, NJView Profile , Will Hill AT&T Labs - Research, 180 Park Avenue, P.O. Box 971, Florham Park, NJ AT&T Labs - Research, 180 Park Avenue, P.O. Box 971, Florham Park, NJView Profile , Deborah Hix Department of Computer Science, Virginia Tech, Blacksburg, VA Department of Computer Science, Virginia Tech, Blacksburg, VAView Profile Authors Info & Claims UIST '00: Proceedings of the 13th annual ACM symposium on User interface software and technologyNovember 2000 Pages 201–209https://doi.org/10.1145/354401.354771Online:01 November 2000Publication History 19citation728DownloadsMetricsTotal Citations19Total Downloads728Last 12 Months21Last 6 weeks3 Get Citation AlertsNew Citation Alert added!This alert has been successfully added and will be sent to:You will be notified whenever a record that you have chosen has been cited.To manage your alert preferences, click on the button below.Manage my AlertsNew Citation Alert!Please log in to your account Save to BinderSave to BinderCreate a New BinderNameCancelCreateExport CitationPublisher SiteGet Access

Topic management is the task of gathering, evaluating, organizing, and sharing a set of web sites for a specific topic. Current web tools do not provide adequate support for this task. We created the TopicShop system to address this need. TopicShop includes (1) a webcrawler that discovers relevant web sites and builds site profiles, and (2) user interfaces for exploring and organizing sites. We conducted an empirical study comparing user performance with TopicShop vs. YahooTM. TopicShop subjects found over 80% more high-quality sites (where quality was determined by independent expert judgements) while browsing only 8 1% as many sites and completing their task in 89% of the time. The site profile data that TopicShop provides - in particular, the number of pages on a site and the number of other sites that link to it - was the key to these results, as users exploited it to identify the most promising sites quickly and easily.

The ever-increasing power of computers and hardware rendering systems has, to date, primarily motivated the creation of visually rich and perceptually realistic virtual environment (VE) applications. Comparatively very little effort has been expended on the user interaction components of VEs. As a result, VE user interfaces are often poorly designed and are rarely evaluated with users. Although usability engineering is a newly emerging facet of VE development, user-centered design and usability evaluation in VEs as a practice still lags far behind what is needed. This paper presents a structured, iterative approach for the user-centered design and evaluation of VE user interaction. This approach consists of the iterative use of expert heuristic evaluation, followed by formative usability evaluation, followed by summative evaluation. We describe our application of this approach to a real-world VE for battlefield visualization, describe the resulting series of design iterations, and present evidence that this approach provides a cost-effective strategy for assessing and iteratively improving user interaction design in VEs. This paper is among the first to report applying an iterative, structured, user-centered design and evaluation approach to VE user interaction design.

A digital library of computer science literature, Envision provides powerful information visualization by displaying search results as a matrix of icons, with layout semantics under user control.Envision's Graphic View interacts with an Item Summary Window giving users access to bibliographic information, and XMosaic provides access to complete bibliographic information, abstracts, and full content.While many visualization interfaces for information retrieval systems depict ranked query-document similarity, Envision graphically presents a variety of document characteristics and supports an extensive range of user tasks.Formative usability evaluation results show great user satisfaction with Envision's style of presentation and the document characteristics visualized.

Pre-screen projection is a new interaction technique that allows a user to pan and zoom integrally through a scene simply by moving his or her head relative to the screen. The underlying concept is based on real-world visual perception, namely, the fact that a person’s view changes as the head moves. Pre-screen projection tracks a user’s head in three dimensions and alters the display on the screen relative to head position, giving a natural perspective effect in response to a user’s head movements. Specifically, projection of a virtual scene is calculated as if the scene were in front of the screen. As a result, the visible scene displayed on the physical screen expands (zooms) dramatically as a user moves nearer. This is analogous to the real world, where the nearer an object is, the more rapidly it visually expands as a person moves toward it. Further, with pre-screen projection a user can navigate (pan and zoom) around a scene integrally, as one unified activity, rather than performing panning and zooming as separate tasks. This paper describes the technique, the real-world metaphor on which it is conceptually based, issues involved in iterative development of the technique, and our approach to its empirical evaluation in a realistic application testbed.

Article Free Access Share on Development and evaluation of a taxonomical model of behavioral representation techniques Authors: J. D. Chase Department of Computer Science, Virginia Tech, Blacksburg VA Department of Computer Science, Virginia Tech, Blacksburg VAView Profile , Robert S. Schulman Department of Statistics, Virginia Tech, Blacksburg VA Department of Statistics, Virginia Tech, Blacksburg VAView Profile , H. Rex Hartson Department of Computer Science, Virginia Tech, Blacksburg VA Department of Computer Science, Virginia Tech, Blacksburg VAView Profile , Deborah Hix Department of Computer Science, Virginia Tech, Blacksburg VA Department of Computer Science, Virginia Tech, Blacksburg VAView Profile Authors Info & Claims CHI '94: Proceedings of the SIGCHI Conference on Human Factors in Computing SystemsApril 1994 Pages 159–165https://doi.org/10.1145/191666.191730Online:24 April 1994Publication History 3citation406DownloadsMetricsTotal Citations3Total Downloads406Last 12 Months20Last 6 weeks8 Get Citation AlertsNew Citation Alert added!This alert has been successfully added and will be sent to:You will be notified whenever a record that you have chosen has been cited.To manage your alert preferences, click on the button below.Manage my AlertsNew Citation Alert!Please log in to your account Save to BinderSave to BinderCreate a New BinderNameCancelCreateExport CitationPublisher SiteeReaderPDF

Project Envision aims to build a “user-centered database from the computer science literature,” initially using the publications of the Association for Computing Machinery (ACM). Accordingly, we have interviewed potential users, as well as experts in library, information, and computer science—to understand their needs, to become aware of their perception of existing information systems, and to collect their recommendations. Design and formative usability evaluation of our interface have been based on those interviews, leading to innovative query formulation and search results screens that work well according to our usability testing. Our development of the Envision database, system software, and protocol for client-server communication builds upon work to identify and represent “objects” that will facilitate reuse and high-level communication of information from author to reader (user). All these efforts are leading not only to a usable prototype digital library but also to a set of nine principles for digital libraries, which we have tried to follow, covering issues of representation, architecture, and interfacing. © 1993 John Wiley & Sons, Inc.

Abstract The Dialogue Management Project at Virginia Tech is studying the poorly understood problem of human‐computer dialogue development. This problem often leads to low usability in human‐computer dialogues. The Dialogue Management Project approaches solutions to low usability in interfaces by addressing human‐computer dialogue development as an integral and equal part of the total system development process. This project consists of two rather distinct, but dependent, parts. One is development of concepts for dialogue management, and the other is implementation of a dialogue management system (DMS) to evaluate these concepts. The goal of this paper is to describe our approach to the development of two of these conceptual aspects and how we oriented those toward the needs of practical implementation. The two conceptual aspects are A structural, descriptive model of human‐computer interaction, and Techniques for representing both the behavioural (end‐user's) view and the constructional (developer's) view of dialogue. The approach to their development was a technology transfer process that was part of a two‐year university/industry research liaison between the Dialogue Management Project and IBM Federal Systems Division (FSD), now called Systems Integration Division. Part of this liaison was aimed at moving our research ideas and results into a real‐world dialogue development environment. Following presentation of the technical problems and solutions, the paper concludes with a discussion of results of our liaison and by raising and addressing some questions of mutual interest that arose during our co‐operative interaction.

Many existing interface representation techniques, especially those associated with UIMS, are constructional and focused on interface implementation, and therefore do not adequately support a user-centered focus. But it is in the behavioral domain of the user that interface designers and evaluators do their work . We are seeking to complement constructional methods by providing a tool-supported technique capable of specifying the behavioral aspects of an interactive system–the tasks and the actions a user performs to accomplish those tasks. In particular, this paper is a practical introduction to use of the User Action Notation (UAN), a task- and user-oriented notation for behavioral representation of asynchronous, direct manipulation interface designs. Interfaces are specified in UAN as a quasihierarchy of asynchronous tasks. At the lower levels, user actions are associated with feedback and system state changes. The notation makes use of visually onomatopoeic symbols and is simple enough to read with little instruction. UAN is being used by growing numbers of interface developers and researchers. In addition to its design role, current research is investigating how UAN can support production and maintenance of code and documentation.

Human-computer interface development tools are interactive systems that support production and execution of the human-computer interface. With their recent proliferation, evaluations and comparisons are constantly done, but without a formal, structured approach. Addressing these problems is difficult, largely because of the relative newness of such tools, because of the many different kinds of systems that are called UIMS, and because of their inherent complexity. These tools are complex because human-computer interfaces, which produce tools, are complex.

The Author's Interactive Dialogue Environment (AIDE) of the Dialogue Management System is an integrated set of direct manipulation tools used by a dialogue author to design and implement human-computer interfaces without writing source code. This paper presents the conceptual dialogue transaction model upon which AIDE is based, describes AIDE, and illustrates how a dialogue author develops an interface using AIDE. A preliminary empirical evaluation of the use of AIDE versus the use of a programming language to implement an interface shows very encouraging results.