Open access spatial data and collaboration

On 19 June 2015, representatives from over 40 Australian research institutions gathered in Canberra to launch their Open Data Collections. The one day event, hosted by the Australian National Data Service (ANDS), showcased to government and a range of national stakeholders the rich variety of data collections that have been generated through the Major Open Data Collections (MODC) project. Colin Eustace attended the showcase for QUT Library and presented a poster that reflected the work that he and Jodie Vaughan generated through the project. QUT’s Blueprint 4, the University’s five-year institutional strategic plan, outlines the key priorities of developing a commitment to working in partnership with industry, as well as combining disciplinary strengths with interdisciplinary application. The Division of Technology, Information and Learning Support (TILS) has undertaken a number of Australian National Data Service (ANDS) funded projects since 2009 with the aim of developing improved research data management services within the University to support these strategic aims. By leveraging existing tools and systems developed during these projects, the Major Open Data Collection (MODC) project delivered support to multi-disciplinary collaborative research activities through partnership building between QUT researchers and Queensland government agencies, in order to add to and promote the discovery and reuse of a collection of spatially referenced datasets. The MODC project built upon existing Research Data Finder infrastructure (which uses VIVO open source software, developed by Cornell University) to develop a separate collection, Spatial Data Finder (https://researchdatafinder.qut.edu.au/spatial) as the interface to display the spatial data collection. During the course of the project, 62 dataset descriptions were added to Spatial Data Finder, 7 added to Research Data Finder and two added to Software Finder, another separate collection. The project team met with 116 individual researchers and attended 13 school and faculty meetings to promote the MODC project and raise awareness of the Library’s services and resources for research data management.

Substation Automation Systems – Future possibilities for commissioning

Substation Automation Systems have undergone many transformational changes triggered by improvements in technologies. Prior to the digital era, it made sense to confirm that the physical wiring matched the schematic design by meticulous and laborious point to point testing. In this way, human errors in either the design or the construction could be identified and fixed prior to entry into service. However, even though modern secondary systems today are largely computerised, we are still undertaking commissioning testing using the same philosophy as if each signal were hard wired. This is slow and tedious and doesn’t do justice to modern computer systems and software automation. One of the major architectural advantages of the IEC 61850 standard is that it “abstracts” the definition of data and services independently of any protocol allowing the mapping of them to any protocol that can meet the modelling and performance requirements. On this basis, any substation element can be defined using these common building blocks and are made available at the design, configuration and operational stages of the system. The primary advantage of accessing data using this methodology rather than the traditional position method (such as DNP 3.0) is that generic tools can be created to manipulate data. Self-describing data contains the information that these tools need to manipulate different data types correctly. More importantly, self-describing data makes the interface between programs robust and flexible. This paper proposes that the improved data definitions and methods for dealing with this data within a tightly bound and compliant IEC 61850 Substation Automation System could completely revolutionise the need to test systems when compared to traditional point to point methods. Using the outcomes of an undergraduate thesis project, we can demonstrate with some certainty that it is possible to automatically test the configuration of a protection relay by comparing the IEC 61850 configuration extracted from the relay against its SCL file for multiple relay vendors. The software tool provides a quick and automatic check that the data sets on a particular relay are correct according to its CID file, thus ensuring that no unexpected modifications are made at any stage of the commissioning process. This tool has been implemented in a Java programming environment using an open source IEC 61850 library to facilitate the server-client association with the relay.

Using competences and competence tools in workforce development

The NHS Knowledge and Skills Framework (KSF) has been a driving force in the move to competence-based workforce development in the NHS. Skills for Health has developed national workforce competences that aim to improve behavioural performance, and in turn increase productivity. This article describes five projects established to test Skills for Health national workforce competences, electronic tools and products in different settings in the NHS. Competences and competence tools were used to redesign services, develop job roles, identify skills gaps and develop learning programmes. Reported benefits of the projects included increased clarity and a structured, consistent and standardized approach to workforce development. Findings from the evaluation of the tools were positive in terms of their overall usefulness and provision of related training/support. Reported constraints of using the competences and tools included issues relating to their availability, content and organization. It is recognized that a highly skilled and flexible workforce is important to the delivery of high-quality health care. These projects suggest that Skills for Health competences can be used as a 'common currency' in workforce development in the UK health sector. This would support the need to adapt rapidly to changing service needs.

Visualization tools for high angular resolution diffusion imaging

There is a major effort in medical imaging to develop algorithms to extract information from DTI and HARDI, which provide detailed information on brain integrity and connectivity. As the images have recently advanced to provide extraordinarily high angular resolution and spatial detail, including an entire manifold of information at each point in the 3D images, there has been no readily available means to view the results. This impedes developments in HARDI research, which need some method to check the plausibility and validity of image processing operations on HARDI data or to appreciate data features or invariants that might serve as a basis for new directions in image segmentation, registration, and statistics. We present a set of tools to provide interactive display of HARDI data, including both a local rendering application and an off-screen renderer that works with a web-based viewer. Visualizations are presented after registration and averaging of HARDI data from 90 human subjects, revealing important details for which there would be no direct way to appreciate using conventional display of scalar images.

Introduction to the Proceedings of the Workshop on User-Focused Service Engineering, Consumption and Aggregation (USECA) 2011

The first User-Focused Service Engineering, Consumption and Aggregation workshop (USECA) in 2011 was held in conjunction with the WISE 2011 conference in Sydney, Australia. Web services and related technology are a widely accepted standard architectural paradigm for application development. The idea of reusing existing software components to build new applications has been well documented and supported for the world of enterprise computing and professional developers. However, this powerful idea has not been transferred to end-users who have limited or no computing knowledge. The current methodologies, models, languages and tools developed for Web service composition are suited to IT professionals and people with years of training in computing technologies. It is still hard to imagine any of these technologies being used by business professionals, as opposed to computing professionals. © 2013 Springer-Verlag.

RNASeqBrowser: A genome browser for simultaneous visualization of raw strand specific RNAseq reads and UCSC genome browser custom tracks

Background Strand specific RNAseq data is now more common in RNAseq projects. Visualizing RNAseq data has become an important matter in Analysis of sequencing data. The most widely used visualization tool is the UCSC genome browser that introduced the custom track concept that enabled researchers to simultaneously visualize gene expression at a particular locus from multiple experiments. Our objective of the software tool is to provide friendly interface for visualization of RNAseq datasets. Results This paper introduces a visualization tool (RNASeqBrowser) that incorporates and extends the functionality of the UCSC genome browser. For example, RNASeqBrowser simultaneously displays read coverage, SNPs, InDels and raw read tracks with other BED and wiggle tracks -- all being dynamically built from the BAM file. Paired reads are also connected in the browser to enable easier identification of novel exon/intron borders and chimaeric transcripts. Strand specific RNAseq data is also supported by RNASeqBrowser that displays reads above (positive strand transcript) or below (negative strand transcripts) a central line. Finally, RNASeqBrowser was designed for ease of use for users with few bioinformatic skills, and incorporates the features of many genome browsers into one platform. Conclusions The features of RNASeqBrowser: (1) RNASeqBrowser integrates UCSC genome browser and NGS visualization tools such as IGV. It extends the functionality of the UCSC genome browser by adding several new types of tracks to show NGS data such as individual raw reads, SNPs and InDels. (2) RNASeqBrowser can dynamically generate RNA secondary structure. It is useful for identifying non-coding RNA such as miRNA. (3) Overlaying NGS wiggle data is helpful in displaying differential expression and is simple to implement in RNASeqBrowser. (4) NGS data accumulates a lot of raw reads. Thus, RNASeqBrowser collapses exact duplicate reads to reduce visualization space. Normal PC’s can show many windows of NGS individual raw reads without much delay. (5) Multiple popup windows of individual raw reads provide users with more viewing space. This avoids existing approaches (such as IGV) which squeeze all raw reads into one window. This will be helpful for visualizing multiple datasets simultaneously. RNASeqBrowser and its manual are freely available at http://www.australianprostatecentre.org/research/software/rnaseqbrowser webcite or http://sourceforge.net/projects/rnaseqbrowser/ webcite

A comparison of international and Australian rating tools for sustainability elements of residential property

The Australian housing sector contributes about a fifth of national greenhouse gas (GHG) emissions. GHG emissions contribute to climate change which leads to an increase in the occurrence or intensity of natural disasters and damage of houses. To ensure housing performance in the face of climate change, various rating tools for residential property have been introduced in different countries. The aim of this paper is to present a preliminary comparison between international and Australian rating tools in terms of purpose, use and sustainability elements for residential property. The methodologies used are to review, classify, compare and identify similarities and differences between rating tools. Two international tools, Building Research Establishment Environmental Assessment Methodology (BREEAM) (UK) and Leadership in Energy and Environmental Design for Homes (LEED-Homes) (USA), will be compared to two Australian tools, Green Star – Multi Unit Residential v1 and EnviroDevelopment. All four rating tools include management, energy, water and material aspects. The findings reveal thirteen elements that fall under three categories: spatial planning, occupants’ health and comfort, and environmental conditions. The variations in different tools may result from differences in local prevailing climate. Not all sustainability elements covered by international rating tools are included in the Australian rating tools. The voluntary nature of the tools implies they are not broadly applied in their respective market and that there is a policy implementation gap. A comprehensive rating tool could be developed in Australia to promote and lessen the confusion about sustainable housing, which in turn assist in improving the supply and demand of sustainable housing.

Comparison of sustainable community rating tools in Australia

The community is the basic unit of urban development, and appropriate assessment tools are needed for communities to evaluate and facilitate decision making concerning sustainable community development and reduce the detrimental effects of urban community actions on the environment. Existing research into sustainable community rating tools focuses primarily on those that are internationally recognized to describe their advantages and future challenges. However, the differences between rating tools due to different regional conditions, situations and characteristics have yet to be addressed. In doing this, this paper examines three sustainable community rating tools in Australia, namely Green Star-Communities PILOT, EnviroDevelopment and VicUrban Sustainability Charter (Master Planned Community Assessment Tool). In order to identify their similarities, differences and advantages these are compared in terms of sustainability coverage, prerequisites, adaptation to locality, scoring and weighting, participation, presentation of results, and application process. These results provide the stakeholders of sustainable community development projects with a better understanding of the available rating tools in Australia and assist with evaluation and decision making.

Technology-mediated tools for shaping experiences in urban commuter trains

This thesis presents the results of a study into ways that technology can be appropriated and designed to support urban rail commuters in their daily journeys. The study evaluated a mobile application prototype deployed along the Brisbane passenger rail network. This prototype was designed to support social interaction between passengers sharing the same trains. This thesis provides a step forward in showing the relevance of increasingly creating solutions that contribute to a more enjoyable and attractive public transport service.

VIP Barcoding: Composition vector-based software for rapid species identification based on DNA barcoding

Species identification based on short sequences of DNA markers, that is, DNA barcoding, has emerged as an integral part of modern taxonomy. However, software for the analysis of large and multilocus barcoding data sets is scarce. The Basic Local Alignment Search Tool (BLAST) is currently the fastest tool capable of handling large databases (e.g. >5000 sequences), but its accuracy is a concern and has been criticized for its local optimization. However, current more accurate software requires sequence alignment or complex calculations, which are time-consuming when dealing with large data sets during data preprocessing or during the search stage. Therefore, it is imperative to develop a practical program for both accurate and scalable species identification for DNA barcoding. In this context, we present VIP Barcoding: a user-friendly software in graphical user interface for rapid DNA barcoding. It adopts a hybrid, two-stage algorithm. First, an alignment-free composition vector (CV) method is utilized to reduce searching space by screening a reference database. The alignment-based K2P distance nearest-neighbour method is then employed to analyse the smaller data set generated in the first stage. In comparison with other software, we demonstrate that VIP Barcoding has (i) higher accuracy than Blastn and several alignment-free methods and (ii) higher scalability than alignment-based distance methods and character-based methods. These results suggest that this platform is able to deal with both large-scale and multilocus barcoding data with accuracy and can contribute to DNA barcoding for modern taxonomy. VIP Barcoding is free and available at http://msl.sls.cuhk.edu.hk/vipbarcoding/.

Business process management as the 'killer app' for Petri nets

Since their inception in 1962, Petri nets have been used in a wide variety of application domains. Although Petri nets are graphical and easy to understand, they have formal semantics and allow for analysis techniques ranging from model checking and structural analysis to process mining and performance analysis. Over time Petri nets emerged as a solid foundation for Business Process Management (BPM) research. The BPM discipline develops methods, techniques, and tools to support the design, enactment, management, and analysis of operational business processes. Mainstream business process modeling notations and workflow management systems are using token-based semantics borrowed from Petri nets. Moreover, state-of-the-art BPM analysis techniques are using Petri nets as an internal representation. Users of BPM methods and tools are often not aware of this. This paper aims to unveil the seminal role of Petri nets in BPM.

Potential uses of Bayesian networks as tools for synthesis of systematic reviews of complex interventions

Bayesian networks (BNs) are tools for representing expert knowledge or evidence. They are especially useful for synthesising evidence or belief concerning a complex intervention, assessing the sensitivity of outcomes to different situations or contextual frameworks and framing decision problems that involve alternative types of intervention. Bayesian networks are useful extensions to logic maps when initiating a review or to facilitate synthesis and bridge the gap between evidence acquisition and decision-making. Formal elicitation techniques allow development of BNs on the basis of expert opinion. Such applications are useful alternatives to ‘empty’ reviews, which identify knowledge gaps but fail to support decision-making. Where review evidence exists, it can inform the development of a BN. We illustrate the construction of a BN using a motivating example that demonstrates how BNs can ensure coherence, transparently structure the problem addressed by a complex intervention and assess sensitivity to context, all of which are critical components of robust reviews of complex interventions. We suggest that BNs should be utilised to routinely synthesise reviews of complex interventions or empty reviews where decisions must be made despite poor evidence.

Collaborative learning from distributed places and spaces: Exploring the use of virtual collaborative tools for local and global student teamwork projects

Educating responsive graduates. Graduate competencies include reliability, communication skills and ability to work in teams. Students using Collaborative technologies adapt to a new working environment, working in teams and using collaborative technologies for learning. Collaborative Technologies were used not simply for delivery of learning but innovatively to supplement and enrich research-based learning, providing a space for active engagement and interaction with resources and team. This promotes the development of responsive ‘intellectual producers’, able to effectively communicate, collaborate and negotiate in complex work environments. Exploiting technologies. Students use ‘new’ technologies to work collaboratively, allowing them to experience the reality of distributed workplaces incorporating both flexibility and ‘real’ time responsiveness. Students are responsible and accountable for individual and group work contributions in a highly transparent and readily accessible workspace. This experience provides a model of an effective learning tool. Navigating uncertainty and complexity. Collaborative technologies allows students to develop critical thinking and reflective skills as they develop a group product. In this forum students build resilience by taking ownership and managing group work, and navigating the uncertainties and complexities of group dynamics as they constructively and professionally engage in team dialogue and learn to focus on the goal of the team task.

Leveraging of software as a service by small and medium enterprises: Information systems capabilities and organisational complementarities

This research explored how small and medium enterprises can achieve success with software as a service (SaaS) applications from cloud. Based upon an empirical investigation of six growth oriented and early technology adopting small and medium enterprises, this study proposes a SaaS for small and medium enterprise success model with two approaches: one for basic and one for advanced benefits. The basic model explains the effective use of SaaS for achieving informational and transactional benefits. The advanced model explains the enhanced use of software as a service for achieving strategic and transformational benefits. Both models explicate the information systems capabilities and organizational complementarities needed for achieving success with SaaS.

Development of molecular tools for the improvement of transgene expression in sugar cane

Biotechnology has the potential to improve sugar cane, one of the world's major crops for food and fuel. This research describes the detailed characterisation of introns and their potential for enhancing transgene expression in sugar cane via intron-mediated enhancement (IME). IME is a phenomenon whereby an intron enhances gene expression from a promoter. Current knowledge on the mechanism of IME or its potential for enhancing gene expression in sugar cane is limited. A better understanding of the factors responsible for IME will help develop new molecular tools that facilitate high levels of constitutive and tissue-specific gene expression in this crop.