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.

Decision - Support Software Tool Handbook

The road and transport industry in Australia and overseas has come a long way to understanding the impact of road traffic noise on the urban environment. Most road authorities now have guidelines to help assess and manage the impact of road traffic noise on noise-sensitive areas and development. While several economic studies across Australia and overseas have tried to value the impact of noise on property prices, decision-makers investing in road traffic noise management strategies have relatively limited historic data and case studies to go on. The perceived success of a noise management strategy currently relies largely on community expectations at a given time, and is not necessarily based on the analysis of the costs and benefits, or the long-term viability and value to the community of the proposed treatment options. With changing trends in urban design, it is essential that the 'whole-of-life' costs and benefits of noise ameliorative treatment options and strategies be identified and made available for decisionmakers in future investment considerations. For this reason, CRC for Construction Innovation Australia funded a research project, Noise Management in Urban Environments to help decision-makers with future road traffic noise management investment decisions. RMIT University and the Queensland Department of Main Roads (QDMR) have conducted the research work, in collaboration with the Queensland Department of Public Works, ARUP Pty Ltd, and the Queensland University of Technology. The research has formed the basis for the development of a decision-support software tool, and helped collate technical and costing data for known noise amelioration treatment options. We intend that the decision support software tool (DST) should help an investment decision-maker to be better informed of suitable noise ameliorative treatment options on a project-by-project basis and identify likely costs and benefits associated with each of those options. This handbook has been prepared as a procedural guide for conducting a comparative assessment of noise ameliorative options. The handbook outlines the methodology and assumptions adopted in the decision-support framework for the investment decision-maker and user of the DST. The DST has been developed to provide an integrated user-friendly interface between road traffic noise modelling software, the relevant assessment criteria and the options analysis process. A user guide for the DST is incorporated in this handbook.

Integrating hardware and software information flow analyses

Security-critical communications devices must be evaluated to the highest possible standards before they can be deployed. This process includes tracing potential information flow through the device's electronic circuitry, for each of the device's operating modes. Increasingly, however, security functionality is being entrusted to embedded software running on microprocessors within such devices, so new strategies are needed for integrating information flow analyses of embedded program code with hardware analyses. Here we show how standard compiler principles can augment high-integrity security evaluations to allow seamless tracing of information flow through both the hardware and software of embedded systems. This is done by unifying input/output statements in embedded program execution paths with the hardware pins they access, and by associating significant software states with corresponding operating modes of the surrounding electronic circuitry.

Maintaining ERP packaged software : a revelatory case study

For many organizations, maintaining and upgrading enterprise resource planning (ERP) systems (large packaged application software) is often far more costly than the initial implementation. Systematic planning and knowledge of the fundamental maintenance processes and maintenance-related management data are required in order to effectively and efficiently administer maintenance activities. This paper reports a revelatory case study of Government Services Provider (GSP), a high-performing ERP service provider to government agencies in Australia. GSP ERP maintenance-process and maintenance-data standards are compared with the IEEE/EIA 12207 software engineering standard for custom software, also drawing upon published research, to identify how practices in the ERP context diverge from the IEEE standard. While the results show that many best practices reflected in the IEEE standard have broad relevance to software generally, divergent practices in the ERP context necessitate a shift in management focus, additional responsibilities, and different maintenance decision criteria. Study findings may provide useful guidance to practitioners, as well as input to the IEEE and other related standards.

Synchronous learner support for music sequencing software

In the field of music technology there is a distinct focus on networking between spatially disparate locales to improve teaching and learning through real-time communication. This article proposes a new delivery model for learner support based on a review of technical and learning services, pilot research using remote desktops to teach music-sequencing software, and recent education research regarding professional development. A 24/7 delivery model using remote desktops, mobile devices and shared calendars offers a flexible real-time addition to the learner support services already on offer. Treating every user of the service as a potential expert, the model aims to deliver universal support situated in a personalized context, which will serve the technical and education requirements of teachers and learners.

Designing participation in agile ridesharing with mobile social software

Growing participation is a key challenge for the viability of sustainability initiatives, many of which require enactment at a local community level in order to be effective. This paper undertakes a review of technology assisted carpooling in order to understand the challenge of designing participation and consider how mobile social software and interface design can be brought to bear. It was found that while persuasive technology and social networking approaches have roles to play, critical factors in the design of carpooling are convenience, ease of use and fit with contingent circumstances, all of which require a use-centred approach to designing a technological system and building participation. Moreover, the reach of technology platform-based global approaches may be limited if they do not cater to local needs. An approach that focuses on iteratively designing technology to support and grow mobile social ridesharing networks in particular locales is proposed. The paper contributes an understanding of HCI approaches in the context of other designing participation approaches.

Getting Excited About Software Programming

Invited one hour presentation at Microsoft Tech Ed 2009 about getting students interested in games programming at QUT.

Introducing a Business Process and Software Centric Approach for Enterprise System Teaching

To meet new challenges of Enterprise Systems that essentially go beyond the initial implementation, contemporary organizations seek employees with business process experts with software skills. Despite a healthy demand from the industry for such expertise, recent studies reveal that most Information Systems (IS) graduates are ill-equipped to meet the challenges of modern organizations. This paper shares insights and experiences from a course that is designed to provide a business process centric view of a market leading Enterprise System. The course, designed for both undergraduate and graduate students, uses two common business processes in a case study that employs both sequential and explorative exercises. Student feedback gained through two longitudinal surveys across two phases of the course demonstrates promising signs of the teaching approach.

An adaptable framework for the teaching and assessment of software development across year levels

Few frameworks exist for the teaching and assessment of programming subjects that are coherent and logical. Nor are they sufficiently generic and adaptable to be used outside the particular tertiary institutions in which they were developed. This paper presents the Teaching and Assessment of Software Development (TASD) frame-work. We describe its development and implementation at an Australian university and demonstrate, with examples, how it has been used, with supporting data. Extracts of criteria sheets (grading rubrics) for a variety of assessment tasks are included. The numerous advantages of this new framework are discussed with comparisons made to those reported in the published literature.

Groundwater Visualisation System (GVS): a software framework for developing low-end, scalable and robust software for 3D visualisation and animation of groundwater conceptual models

Effective management of groundwater requires stakeholders to have a realistic conceptual understanding of the groundwater systems and hydrological processes.However, groundwater data can be complex, confusing and often difficult for people to comprehend..A powerful way to communicate understanding of groundwater processes, complex subsurface geology and their relationships is through the use of visualisation techniques to create 3D conceptual groundwater models. In addition, the ability to animate, interrogate and interact with 3D models can encourage a higher level of understanding than static images alone. While there are increasing numbers of software tools available for developing and visualising groundwater conceptual models, these packages are often very expensive and are not readily accessible to majority people due to complexity. .The Groundwater Visualisation System (GVS) is a software framework that can be used to develop groundwater visualisation tools aimed specifically at non-technical computer users and those who are not groundwater domain experts. A primary aim of GVS is to provide management support for agencies, and enhancecommunity understanding.

Approach to developing a 3D conceptual hydrogeology model, in a system with multiple bore logs, Howard East, Darwin, using in-house software (GVS)

The Howard East rural area has experienced a rapid growth of small block subdivisions and horticulture over the last 40 years, which has been based on groundwater supply. Early bores in the area provide part of the water supply for Darwin City and are maintained and monitored by NT Power & Water Corporation. The Territory government (NRETAS) has established a monitoring network, and now 48 bores are monitored. However, in the area there are over 2700 private bores that are unregulated.Although NRETAS has both FDM and FEM simulations for the region, community support for potential regulation is sought. To improve stakeholder understanding of the resource QUT was retained by the TRaCKconsortium to develop a 3D visualisation of the groundwater system.