BioPatML : pattern sharing for the genomic sciences

Computational biology increasingly demands the sharing of sophisticated data and annotations between research groups. Web 2.0 style sharing and publication requires that biological systems be described in well-defined, yet flexible and extensible formats which enhance exchange and re-use. In contrast to many of the standards for exchange in the genomic sciences, descriptions of biological sequences show a great diversity in format and function, impeding the definition and exchange of sequence patterns. In this presentation, we introduce BioPatML, an XML-based pattern description language that supports a wide range of patterns and allows the construction of complex, hierarchically structured patterns and pattern libraries. BioPatML unifies the diversity of current pattern description languages and fills a gap in the set of XML-based description languages for biological systems. We discuss the structure and elements of the language, and demonstrate its advantages on a series of applications, showing lightweight integration between the BioPatML parser and search engine, and the SilverGene genome browser. We conclude by describing our site to enable large scale pattern sharing, and our efforts to seed this repository.

Listening to nature : techniques for large-scale monitoring of ecosystems using acoustics

Climate change and human activity are subjecting the environment to unprecedented rates of change. Monitoring these changes is an immense task that demands new levels of automated monitoring and analysis. We propose the use of acoustics as a proxy for the time consuming auditing of fauna, especially for determining the presence/absence of species. Acoustic monitoring is deceptively simple; seemingly all that is required is a sound recorder. However there are many major challenges if acoustics are to be used for large scale monitoring of ecosystems. Key issues are scalability and automation. This paper discusses our approach to this important research problem. Our work is being undertaken in collaboration with ecologists interested both in identifying particular species and in general ecosystem health.

Listening to nature : acoustic monitoring of the environment

The requirement to monitor the rapid pace of environmental change due to global warming and to human development is producing large volumes of data but placing much stress on the capacity of ecologists to store, analyse and visualise that data. To date, much of the data has been provided by low level sensors monitoring soil moisture, dissolved nutrients, light intensity, gas composition and the like. However, a significant part of an ecologist’s work is to obtain information about species diversity, distributions and relationships. This task typically requires the physical presence of an ecologist in the field, listening and watching for species of interest. It is an extremely difficult task to automate because of the higher order difficulties in bandwidth, data management and intelligent analysis if one wishes to emulate the highly trained eyes and ears of an ecologist. This paper is concerned with just one part of the bigger challenge of environmental monitoring – the acquisition and analysis of acoustic recordings of the environment. Our intention is to provide helpful tools to ecologists – tools that apply information technologies and computational technologies to all aspects of the acoustic environment. The on-line system which we are building in conjunction with ecologists offers an integrated approach to recording, data management and analysis. The ecologists we work with have different requirements and therefore we have adopted the toolbox approach, that is, we offer a number of different web services that can be concatenated according to need. In particular, one group of ecologists is concerned with identifying the presence or absence of species and their distributions in time and space. Another group, motivated by legislative requirements for measuring habitat condition, are interested in summary indices of environmental health. In both case, the key issues are scalability and automation.

Commercialisation of regenerative human tissue : Regulation and reform in Australia and England, Wales and Northern Ireland

The commercialisation of therapeutic products containing regenerative human tissue is regulated by the common law, statute and ethical guidelines in Australia and England, Wales and Northern Ireland. This article examines the regulatory regimes in these jurisdictions and considers whether reform is required to both support scientific research and ensure conformity with modern social views on medical research and the use of human tissue. The authors consider the crucial role of informed consent in striking the balance between the interests of researchers and the interests of the public.

A45 ICT curriculum design to bridge the gap between industry and academia

Building Information Model (BIM) software, collaboration platforms and 5D Construction Management software is now commercially available and presents the opportunity for construction project teams to design more cost effectively, plan construction earlier, manage costs throughout the life cycle of a building project and provide a central asset management register for facilities managers. This paper outlines the merits of taking a holistic view of ICT in curriculum design. The educational barriers to implementation of these models and planning tools are highlighted. Careful choice of computer software can make a significant difference to how quickly students can master skills; how easy it is to study and how much they enjoy learning and be prepared for employment. An argument for BIM and 5D planning tools to be introduced into the curriculum to assist industry increase productivity and efficiencies are outlined by the authors.

Investigating Familiarity in Older Adults to Facilitate Intuitive Interaction

This paper discusses how intuitive interaction is a possible way to increase the efficiency and effectiveness of interaction with older adults. It provides insights into existing research on intuitive interaction, and the role of prior experience and familiarity in intuition. An experiment is discussed which investigates differences in familiarity between younger and older adults. A comprehensive coding system has been developed to help analyse the data collected. This research is currently in progress.

Comparative study of guidelines and practices for building infrastructure asset management

This paper presents a comparative study of primarily Australian (and limited international) practices and guidelines on Buildings Asset Management (BAM). The objective of this study was to identify potential gaps in current practices and potential areas of research for further improvement. The paper starts with an overview of BAM. Later sections cover current BAM practices and guidelines across different states of Australia; give a limited overview of international practices and concludes with the authors’ observations.

Learning Strategies for Digital Tools

Learning a digital tool is often a hidden process. We tend to learn new tools in a bewildering range of ways. Formal, informal, structured, random, conscious, unconscious, individual, group strategies, may all play a part, but are often lost to us in the complex and demanding processes of learning. But when we reflect carefully on the experience, some patterns and surprising techniques emerge. This monograph presents the thinking of seven students in MDN642, Digital Pedagogies, where they have deliberately reflected on the mental processes at work as they learnt a digital technology of their choice.

I-cobb - An innovative technique in spinal radiographic measurement

The measurement of Cobb angles on radiographs of patients with spinal deformities is routine practice in spinal clinics. The technique relies on the use and availability of specialist equipment such as a goniometer, cobbometer or protractor. The aim of this study was to validate the use of i-Phone (Apple Inc) combined with Tilt Meter Pro software as compared to a protractor in the measurement of Cobb angles. The i-Phone combined with Tilt Meter Pro software offers a faster alternative to the traditional method of Cobb angle measurement. The use of i-Phone offers a more convenient way of measuring Cobb angles in the outpatient setting. The intra-observer repeatability of the iPhone is equivalent to the protractor in the measurement of Cobb angles.

The relationship between deformity correction and clinical outcomes after thoracoscopic scoliosis surgery

Surgical treatment of scoliosis is quantitatively assessed in the clinic using radiographic measures of deformity correction, as well as the rib hump, but it is important to understand the extent to which these quantitative measures correlate with self-reported improvements in patients’ quality of life following surgery. The purpose of this prospective study was to evaluate the relationship between clinical outcomes of thoracoscopic anterior scoliosis surgery and deformity correction using the Scoliosis Research Society questionnaire (SRS-24). Patients undergoing thoracoscopic anterior scoliosis correction report good SRS scores which are comparable to those reported in previous studies for both open and thoracoscopic scoliosis correction procedures. Major Cobb correction is a significant predictor of patient satisfaction when comparing subgroups of patients with the highest and lowest major curve corrections.

The effect of insertion time on the axial pullout strength of anterior vertebral body screws

Top screw pullout occurs when the screw is under too much axial force to remain secure in the vertebral body. In vitro biomechanical pullout tests are commonly done to find the maximum fixation strength of anterior vertebral body screws. Typically, pullout tests are done instantaneously where the screw is inserted and then pulled out immediately after insertion. However, bone is a viscoelastic material so it shows a time dependent stress and strain response. Because of this property, it was hypothesised that creep occurs in the vertebral trabecular bone due to the stress caused by the screw. The objective of this study was therefore to determine whether the axial pullout strength of anterior vertebral body screws used for scoliosis correction surgery changes with time after insertion. This study found that there is a possible relationship between pullout strength and time; however more testing is required as the sample numbers were quite small. The design of the screw is made with the knowledge of the strength it must obtain. This is important to prevent such occurrences as top screw pullout. If the pullout strength is indeed decreased due to creep, the design of the screw may need to be changed to withstand greater forces.

Effects of fare collection policy on operating characteristics of a Brisbane busway station

Transit agencies across the world are increasingly shifting their fare collection mechanisms towards fully automated systems like the smart card. One of the objectives in implementing such a system is to reduce the boarding time per passenger and hence reduce the overall dwell time for the buses at the bus stops/bus rapid transit (BRT) stations. TransLink, the transit authority responsible for public transport management in South East Queensland, has introduced ‘GoCard’ technology using the Cubic platform for fare collection on its public transport system. In addition to this, three inner city BRT stations on South East Busway spine are operating as pre-paid platforms during evening peak time. This paper evaluates the effects of these multiple policy measures on operation of study busway station. The comparison between pre and post policy scenarios suggests that though boarding time per passenger has decreased, while the alighting time per passenger has increased slightly. However, there is a substantial reduction in operating efficiency was observed at the station.

Towards a building sustainability assessment framework

This paper provides an overview of a new framework for a design stage Building Environmental Assessment (BEA) tool and a discussion of strategic responses to existing tool issues and relative stakeholder requirements that lead to the development of this tool founded on new information and communication technology (ICT) related to developments in 3D CAD technology. After introducing the context of the BEA and some of their team’s new work the authors • Critique current BEA tool theory; • Review previous assessments of stakeholder needs; • Introduce a new framework applied to analyse such tools • Highlight and key results considering illustrative ICT capabilities and • Discuss their potential significance upon BEA tool stakeholders.

Innovative cartography standards for Web-GIS portals : case study of the 'Survey of Israel's' Web-GIS Portal

Maps have been published on the world wide web since its inception (Cartwright, 1999) and are still accessed and viewed by millions of users today (Peterson, 2003). While early webbased GIS products lacked a complete set of cartographic capabilities, the functionality within such systems has significantly increased over recent years. Functionalities once found only in desktop GIS products are now available in web-based GIS applications, for example, data entry, basic editing, and analysis. Applications based on web-GIS are becoming more widespread and the web-based GIS environment is replacing the traditional desktop GIS platforms in many organizations. Therefore, development of a new cartographic method for web-based GIS is vital. The broad aim of this project is to examine and discuss the challenges and opportunities of innovative cartography methods for web-based GIS platforms. The work introduces a recently developed cartographic methodology, which is based on a web-based GIS portal by the Survey of Israel (SOI). The work discusses the prospects and constraints of such methods in improving web-GIS interfaces and usability for the end user. The work also tables the preliminary findings of the initial implementation of the web-based GIS cartographic method within the portal of the Survey of Israel, as well as the applicability of those methods elsewhere.

Literacy and identity : examining the metaphors in history and contemporary research

In this review, the authors interrogate the recent identity turn in literacy studies by asking the following: How do particular views of identity shape how researchers think about literacy and, conversely, how does the view of literacy taken by a researcher shape meanings made about identity? To address this question, the authors review various ways of conceptualizing identity by using five metaphors for identity documented in the identity literature: identity as (1) difference, (2) sense of self/subjectivity, (3) mind or consciousness, (4) narrative, and (5) position. Few literacy studies have acknowledged this range of perspectives on and views for conceptualizing identity and yet, subtle differences in identity theories have widely different implications for how one thinks about both how literacy matters to identity and how identity matters to literacy. The authors offer this review to encourage more theorizing of both literacy and identity as social practices and, most important, of how the two breathe life into each other.