A web application to perform linkage disequilibrium and linkage analyses on a computational grid

Motivation: Unravelling the genetic architecture of complex traits requires large amounts of data, sophisticated models and large computational resources. The lack of user-friendly software incorporating all these requisites is delaying progress in the analysis of complex traits. Methods: Linkage disequilibrium and linkage analysis (LDLA) is a high-resolution gene mapping approach based on sophisticated mixed linear models, applicable to any population structure. LDLA can use population history information in addition to pedigree and molecular markers to decompose traits into genetic components. Analyses are distributed in parallel over a large public grid of computers in the UK. Results: We have proven the performance of LDLA with analyses of simulated data. There are real gains in statistical power to detect quantitative trait loci when using historical information compared with traditional linkage analysis. Moreover, the use of a grid of computers significantly increases computational speed, hence allowing analyses that would have been prohibitive on a single computer. © The Author 2009. Published by Oxford University Press. All rights reserved.

Not losing the plot : creating, collecting and curating qualitative data through a web-based application

Collecting regular personal reflections from first year teachers in rural and remote schools is challenging as they are busily absorbed in their practice, and separated from each other and the researchers by thousands of kilometres. In response, an innovative web-based solution was designed to both collect data and be a responsive support system for early career teachers as they came to terms with their new professional identities within rural and remote school settings. Using an emailed link to a web-based application named goingok.com, the participants are charting their first year plotlines using a sliding scale from ‘distressed’, ‘ok’ to ‘soaring’ and describing their self-assessment in short descriptive posts. These reflections are visible to the participants as a developing online journal, while the collections of de-identified developing plotlines are visible to the research team, alongside numerical data. This paper explores important aspects of the design process, together with the challenges and opportunities encountered in its implementation. A number of the key considerations for choosing to develop a web application for data collection are initially identified, and the resultant application features and scope are then examined. Examples are then provided about how a responsive software development approach can be part of a supportive feedback loop for participants while being an effective data collection process. Opportunities for further development are also suggested with projected implications for future research.

All the worldwide web's a stage : teenage girls' self-presentation and identities formation through status updates

This study investigates grade eight girls’ use of status updates on Facebook in order to create identities online. Using sociologist Erving Goffman’s theory of self-presentation as a framework, Jones and Pittman’s subsequent strategies of self-presentation are used to discover the ways in which teenage girls use status updates in order to create identities online and manage audience impressions. Using a mixed methods design, the results showed that, while existing self-presentation strategies persist, social networking has created new means of self-presentation. This study adds to a growing pool of research regarding teens’ engagement with social networking websites to form identities.

Encounters and content sharing in an urban village : reading texts through an archaeological lens

Archaeology provides a framework of analysis and interpretation that is useful for disentangling the textual layers of a contemporary lived-in urban space. The producers and readers of texts may include those who planned and developed the site and those who now live, visit and work there. Some of the social encounters and content sharing between these people may be artificially produced or manufactured in the hope that certain social situations will occur. Others may be serendipitous. With archaeology’s original focus on places that are no longer inhabited it is often only the remaining artefacts and features of the built environment that form the basis for interpreting the social relationships of past people. Our analysis however, is framed within a contemporary notion of archaeological artefacts in an urban setting. Unlike an excavation, where the past is revealed through digging into the landscape, the application of landscape archaeology within a present day urban context is necessarily more experiential, visual and based on recording and analysing the physical traces of social encounters and relationships between residents and visitors. These physical traces are present within the creative content, and the built and natural elements of the environment. This chapter explores notions of social encounters and content sharing in an urban village by analysing three different types of texts: the design of the built environment; content produced by residents through a geospatial web application; and, print and online media produced in digital storytelling workshops.

Automatic generation of effective video summaries

As the popularity of video as an information medium rises, the amount of video content that we produce and archive keeps growing. This creates a demand for shorter representations of videos in order to assist the task of video retrieval. The traditional solution is to let humans watch these videos and write textual summaries based on what they saw. This summarisation process, however, is time-consuming. Moreover, a lot of useful audio-visual information contained in the original video can be lost. Video summarisation aims to turn a full-length video into a more concise version that preserves as much information as possible. The problem of video summarisation is to minimise the trade-off between how concise and how representative a summary is. There are also usability concerns that need to be addressed in a video summarisation scheme. To solve these problems, this research aims to create an automatic video summarisation framework that combines and improves on existing video summarisation techniques, with the focus on practicality and user satisfaction. We also investigate the need for different summarisation strategies in different kinds of videos, for example news, sports, or TV series. Finally, we develop a video summarisation system based on the framework, which is validated by subjective and objective evaluation. The evaluation results shows that the proposed framework is effective for creating video skims, producing high user satisfaction rate and having reasonably low computing requirement. We also demonstrate that the techniques presented in this research can be used for visualising video summaries in the form web pages showing various useful information, both from the video itself and from external sources.

Extending Web Modeling Language to exploit stigmergy : intentionally recording unintentional trails

Software development and Web site development techniques have evolved significantly over the past 20 years. The relatively young Web Application development area has borrowed heavily from traditional software development methodologies primarily due to the similarities in areas of data persistence and User Interface (UI) design. Recent developments in this area propose a new Web Modeling Language (WebML) to facilitate the nuances specific to Web development. WebML is one of a number of implementations designed to enable modeling of web site interaction flows while being extendable to accommodate new features in Web site development into the future. Our research aims to extend WebML with a focus on stigmergy which is a biological term originally used to describe coordination between insects. We see design features in existing Web sites that mimic stigmergic mechanisms as part of the UI. We believe that we can synthesize and embed stigmergy in Web 2.0 sites. This paper focuses on the sub-topic of site UI design and stigmergic mechanism designs required to achieve this.

BioCondition assessment tool : a mobile application to aid vegetation assessment

Environmental degradation has become increasingly aggressive in recent years due to rapid urban development and other land use pressures. This chapter looks at BioCondition, a newly developed vegetation assessment framework by Queensland Department of Resource Management (DERM) and how mobile technology can assist beginners in conducting the survey. Even though BioCondition is designed to be simple, it is still fairly inaccessible to beginners due to its complex, time consuming, and repetitive nature. A Windows Phone mobile application, BioCondition Assessment Tool, was developed to provide on-site guidance to beginners and document the assessment process for future revision and comparison. The application was tested in an experiment at Samford Conservation Park with 12 students studying ecology in Queensland University of Technology.

Secure modular password authentication for the web using channel bindings

Secure protocols for password-based user authentication are well-studied in the cryptographic literature but have failed to see wide-spread adoption on the Internet; most proposals to date require extensive modifications to the Transport Layer Security (TLS) protocol, making deployment challenging. Recently, a few modular designs have been proposed in which a cryptographically secure password-based mutual authentication protocol is run inside a confidential (but not necessarily authenticated) channel such as TLS; the password protocol is bound to the established channel to prevent active attacks. Such protocols are useful in practice for a variety of reasons: security no longer relies on users' ability to validate server certificates and can potentially be implemented with no modifications to the secure channel protocol library. We provide a systematic study of such authentication protocols. Building on recent advances in modelling TLS, we give a formal definition of the intended security goal, which we call password-authenticated and confidential channel establishment (PACCE). We show generically that combining a secure channel protocol, such as TLS, with a password authentication protocol, where the two protocols are bound together using either the transcript of the secure channel's handshake or the server's certificate, results in a secure PACCE protocol. Our prototype based on TLS is available as a cross-platform client-side Firefox browser extension and a server-side web application which can easily be installed on deployed web browsers and servers.

Patient perspectives of using a web based intervention program for patients with type 2 diabetes and acute coronary syndrome

Introduction Research highlights patients with dual diagnoses of type 2 diabetes and acute coronary syndrome (ACS) have higher readmission rates and poorer health outcomes than patients with singular chronic conditions. Despite this, there is a lack of education programs targeted for this dual diagnosis population to improve self-management and decrease negative health outcomes. There is evidence to suggest that internet based interventions may improve health outcomes for patients with singular chronic conditions, however there is a need to develop an evidence base for ACS patients with comorbid diabetes. There is a growing awareness of the importance of a participatory model in developing effective online interventions. That is, internet interventions are more effective if end users’ perceptions of the intervention are incorporated in their final development prior to testing in large scale trials. Objectives This study investigated patients’ perspectives of the web-based intervention designed to promote self-management of the dual conditions in order to refine the intervention prior to clinical trial evaluation. Methods An interpretive approach with thematic analysis was used to obtain deeper understanding regarding participants’ experience when using web-application interventions for patients with ACS and type 2 diabetes. Semi-structured interviews were undertaken on a purposive sample of 30 patients meeting strict inclusion and exclusion criteria to obtain their perspectives on the program. Results Preliminary results indicate patients with dual diagnoses express more complex needs than those with a singular condition. Participants express a positive experience with the proposed internet intervention and emerging themes include that the web page is seen as easy to use and comforting as a support, in that patients know they are not alone. Further results will be reported as they become available. Conclusion The results indicate potential for patient acceptability of the newly developed internet intervention for patients with ACS and comorbid diabetes. Incorporation of patient perspectives into the final development of the intervention is likely to maximise successful outcomes of any future trials that utilise this intervention. Future quantitative evaluation of the effectiveness of the intervention is being planned.

Vote as you go : Blending interfaces for community engagement into the urban space

This paper presents a series of studies on situated interfaces for community engagement. Firstly, we identify five recurring design challenges as well as four common strategies used to overcome them. We then assess the effectiveness of these strategies through field studies with public polling interfaces. We developed two very different polling interfaces in the form of (1) a web application running on an iPad mounted on a stand, allowing one vote at a time, and (2) a playful full-body interaction application for a large urban screen allowing concurrent participation. We deployed both interfaces in an urban precinct with high pedestrian traffic and equipped with a large urban screen. Analysing discoverability and learnability of each scenario, we derive insights regarding effective ways of blending community engagement interfaces into the built environment, while attracting the attention of passers-by and communicating the results of civic participation.

A distributed denial of service testbed

The Denial of Service Testing Framework (dosTF) being developed as part of the joint India-Australia research project for ‘Protecting Critical Infrastructure from Denial of Service Attacks’ allows for the construction, monitoring and management of emulated Distributed Denial of Service attacks using modest hardware resources. The purpose of the testbed is to study the effectiveness of different DDoS mitigation strategies and to allow for the testing of defense appliances. Experiments are saved and edited in XML as abstract descriptions of an attack/defense strategy that is only mapped to real resources at run-time. It also provides a web-application portal interface that can start, stop and monitor an attack remotely. Rather than monitoring a service under attack indirectly, by observing traffic and general system parameters, monitoring of the target application is performed directly in real time via a customised SNMP agent.

Structural reliability prediction of a steel bridge element using Dynamic Object Oriented Bayesian Network (DOOBN)

Different from conventional methods for structural reliability evaluation, such as, first/second-order reliability methods (FORM/SORM) or Monte Carlo simulation based on corresponding limit state functions, a novel approach based on dynamic objective oriented Bayesian network (DOOBN) for prediction of structural reliability of a steel bridge element has been proposed in this paper. The DOOBN approach can effectively model the deterioration processes of a steel bridge element and predict their structural reliability over time. This approach is also able to achieve Bayesian updating with observed information from measurements, monitoring and visual inspection. Moreover, the computational capacity embedded in the approach can be used to facilitate integrated management and maintenance optimization in a bridge system. A steel bridge girder is used to validate the proposed approach. The predicted results are compared with those evaluated by FORM method.

Design of decoupling networks for circulant symmetric antenna arrays

Small element spacing in compact arrays results in strong mutual coupling between array elements. Performance degradation associated with the strong coupling can be avoided through the introduction of a decoupling network consisting of interconnected reactive elements. We present a systematic design procedure for decoupling networks of symmetrical arrays with more than three elements and characterized by circulant scattering parameter matrices. The elements of the decoupling network are obtained through repeated decoupling of the characteristic eigenmodes of the array, which allows the calculation of element values using closed-form expressions.

Should we still lecture? Reconsidering pedagogical approaches to promote student engagement, challenging the traditional lecture

The dynamic interplay between existing learning frameworks: people, pedagogy, learning spaces and technology is challenging the traditional lecture. A paradigm is emerging from the correlation of change amongst these elements, offering new possibilities for improving the quality of the learning experience. For many universities, the design of physical learning spaces has been the focal point for blending technology and flexible learning spaces to promote learning and teaching. As the pace of technological change intensifies, affording new opportunities for engaging learners, pedagogical practice in higher education is not comparatively evolving. The resulting disparity is an opportunity for the reconsideration of pedagogical practice for increased student engagement in physical learning spaces as an opportunity for active learning. This interplay between students, staff and technology is challenging the value for students in attending physical learning spaces such as the traditional lecture. Why should students attend for classes devoted to content delivery when streaming and web technologies afford more flexible learning opportunities? Should we still lecture? Reconsideration of pedagogy is driving learning design at Queensland University of Technology, seeking new approaches affording increased student engagement via active learning experiences within large lectures. This paper provides an overview and an evaluation of one of these initiatives, Open Web Lecture (OWL), an experimental web based student response application developed by Queensland University of Technology. OWL seamlessly integrates a virtual learning environment within physical learning spaces, fostering active learning opportunities. This paper will evaluate the pilot of this initiative through consideration of effectiveness in increasing student engagement through the affordance of web enabled active learning opportunities in physical learning spaces.