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.

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.

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.

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.

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.

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.

A context sensitive model for querying linked scientific data

This thesis provides a query model suitable for context sensitive access to a wide range of distributed linked datasets which are available to scientists using the Internet. The model is designed based on scientific research standards which require scientists to provide replicable methods in their publications. Although there are query models available that provide limited replicability, they do not contextualise the process whereby different scientists select dataset locations based on their trust and physical location. In different contexts, scientists need to perform different data cleaning actions, independent of the overall query, and the model was designed to accommodate this function. The query model was implemented as a prototype web application and its features were verified through its use as the engine behind a major scientific data access site, Bio2RDF.org. The prototype showed that it was possible to have context sensitive behaviour for each of the three mirrors of Bio2RDF.org using a single set of configuration settings. The prototype provided executable query provenance that could be attached to scientific publications to fulfil replicability requirements. The model was designed to make it simple to independently interpret and execute the query provenance documents using context specific profiles, without modifying the original provenance documents. Experiments using the prototype as the data access tool in workflow management systems confirmed that the design of the model made it possible to replicate results in different contexts with minimal additions, and no deletions, to query provenance documents.

Managing distraction in 21st century learning environments

First year students attend face-to-face classes armed with an arsenal of internet enabled digital devices. The conundrum is that while these devices offer scope for enhancing opportunities for engagement in face-to-face learning, they may simultaneously distract students away from learning and compound isolation issues. This paper considers how to best to use these devices for maximum engagement in first year face-to-face learning so as to assist students in connecting with other learners and instructors within the learning environment

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 services based conference planner application using software agents, grid services and web services

This demonstration highlights the applications of our research work i.e. second generation (Scalable Fault Tolerant Agent Grooming Environment - SAGE) Multi Agent System, Integration of Software Agents and Grid Computing and Autonomous Agent Architecture in the Agent Platform. It is a conference planner application that uses collaborative effort of services deployed geographically wide in different technologies i.e. Software Agents, Grid computing and Web services to perform useful tasks as required. Copyright 2005 ACM.

A collaborative multi-agent based conference planner application using web and grid services

Distributed Collaborative Computing services have taken over centralized computing platforms allowing the development of distributed collaborative user applications. These applications enable people and computers to work together more productively. Multi-Agent System (MAS) has emerged as a distributed collaborative environment which allows a number of agents to cooperate and interact with each other in a complex environment. We want to place our agents in problems whose solutions require the collation and fusion of information, knowledge or data from distributed and autonomous information sources. In this paper we present the design and implementation of an agent based conference planner application that uses collaborative effort of agents which function continuously and autonomously in a particular environment. The application also enables the collaborative use of services deployed geographically wide in different technologies i.e. Software Agents, Grid computing and Web service. The premise of the application is that it allows autonomous agents interacting with web and grid services to plan a conference as a proxy to their owners (humans). © 2005 IEEE.