Creating a legal framework for copyright management of open access within the Australian academic and research sector

This chapter analyses the copyright law framework needed to ensure open access to outputs of the Australian academic and research sector such as journal articles and theses. It overviews the new knowledge landscape, the principles of copyright law, the concept of open access to knowledge, the recently developed open content models of copyright licensing and the challenges faced in providing greater access to knowledge and research outputs.

FaceXpress : an integrated software suite for facial emotion stimulus manipulation and facial measurement

The characterisation of facial expression through landmark-based analysis methods such as FACEM (Pilowsky & Katsikitis, 1994) has a variety of uses in psychiatric and psychological research. In these systems, important structural relationships are extracted from images of facial expressions by the analysis of a pre-defined set of feature points. These relationship measures may then be used, for instance, to assess the degree of variability and similarity between different facial expressions of emotion. FaceXpress is a multimedia software suite that provides a generalised workbench for landmark-based facial emotion analysis and stimulus manipulation. It is a flexible tool that is designed to be specialised at runtime by the user. While FaceXpress has been used to implement the FACEM process, it can also be configured to support any other similar, arbitrary system for quantifying human facial emotion. FaceXpress also implements an integrated set of image processing tools and specialised tools for facial expression stimulus production including facial morphing routines and the generation of expression-representative line drawings from photographs.

Multi-level neural modelling : an application of object-oriented software engineering

Neu-Model, an ongoing project aimed at developing a neural simulation environment that is extremely computationally powerful and flexible, is described. It is shown that the use of good Software Engineering techniques in Neu-Model’s design and implementation is resulting in a high performance system that is powerful and flexible enough to allow rigorous exploration of brain function at a variety of conceptual levels.

Exploring variation in measurement as a foundation for statistical thinking in the elementary school

This study was based on the premise that variation is the foundation of statistics and statistical investigations. The study followed the development of fourth-grade students' understanding of variation through participation in a sequence of two lessons based on measurement. In the first lesson all students measured the arm span of one student, revealing pathways students follow in developing understanding of variation and linear measurement (related to research question 1). In the second lesson each student's arm span was measured once, introducing a different aspect of variation for students to observe and contrast. From this second lesson, students' development of the ability to compare their representations for the two scenarios and explain differences in terms of variation was explored (research question 2). Students' documentation, in both workbook and software formats, enabled us to monitor their engagement and identify their increasing appreciation of the need to observe, represent, and contrast the variation in the data. Following the lessons, a written student assessment was used for judging retention of understanding of variation developed through the lessons and the degree of transfer of understanding to a different scenario (research question 3).

Dynamic agent composition for large-scale agent-based models

PURPOSE: This paper describes dynamic agent composition, used to support the development of flexible and extensible large-scale agent-based models (ABMs). This approach was motivated by a need to extend and modify, with ease, an ABM with an underlying networked structure as more information becomes available. Flexibility was also sought after so that simulations are set up with ease, without the need to program. METHODS: The dynamic agent composition approach consists in having agents, whose implementation has been broken into atomic units, come together at runtime to form the complex system representation on which simulations are run. These components capture information at a fine level of detail and provide a vast range of combinations and options for a modeller to create ABMs. RESULTS: A description of the dynamic agent composition is given in this paper, as well as details about its implementation within MODAM (MODular Agent-based Model), a software framework which is applied to the planning of the electricity distribution network. Illustrations of the implementation of the dynamic agent composition are consequently given for that domain throughout the paper. It is however expected that this approach will be beneficial to other problem domains, especially those with a networked structure, such as water or gas networks. CONCLUSIONS: Dynamic agent composition has many advantages over the way agent-based models are traditionally built for the users, the developers, as well as for agent-based modelling as a scientific approach. Developers can extend the model without the need to access or modify previously written code; they can develop groups of entities independently and add them to those already defined to extend the model. Users can mix-and-match already implemented components to form large-scales ABMs, allowing them to quickly setup simulations and easily compare scenarios without the need to program. The dynamic agent composition provides a natural simulation space over which ABMs of networked structures are represented, facilitating their implementation; and verification and validation of models is facilitated by quickly setting up alternative simulations.

Impact of technology uptake on an Australian electricity distribution network

This paper presents simulation results for future electricity grids using an agent-based model developed with MODAM (MODular Agent-based Model). MODAM is introduced and its use demonstrated through four simulations based on a scenario that expects a rise of on-site renewable generators and electric vehicles (EV) usage. The simulations were run over many years, for two areas in Townsville, Australia, capturing variability in space of the technology uptake, and for two charging methods for EV, capturing people's behaviours and their impact on the time of the peak load. Impact analyses of these technologies were performed over the areas, down to the distribution transformer level, where greater variability of their contribution to the assets peak load was observed. The MODAM models can be used for different purposes such as impact of renewables on grid sizing, or on greenhouse gas emissions. The insights gained from using MODAM for technology assessment are discussed.

A real-time software architecture for robotics and automation

This paper describes a software architecture for real-world robotic applications. We discuss issues of software reliability, testing and realistic off-line simulation that allows the majority of the automation system to be tested off-line in the laboratory before deployment in the field. A recent project, the automation of a very large mining machine is used to illustrate the discussion.

Response of segmented bored transit tunnels to surface blast

Increasing threat of terrorism highlights the importance of enhancing the resilience of underground tunnels to all hazards. This paper develops, applies and compares the Arbitrary Lagrangian Eulerian (ALE) and Smooth Particle Hydrodynamics (SPH) techniques to treat the response of buried tunnels to surface explosions. The results and outcomes of the two techniques were compared, along with results from existing test data. The comparison shows that the ALE technique is a better method for describing the tunnel response for above ground explosion with regards to modeling accuracy and computational efficiency. The ALE technique was then applied to treat the blast response of different types of segmented bored tunnels buried in dry sand. Results indicate that the most used modern ring type segmented tunnels were more flexible for in-plane response, however, they suffered permanent drifts between the rings. Hexagonal segmented tunnels responded with negligible drifts in the longitudinal direction, but the magnitudes of in-plane drifts were large and hence hazardous for the tunnel. Interlocking segmented tunnels suffered from permanent drifts in both the longitudinal and transverse directions. Multi-surface radial joints in both the hexagonal and interlocking segments affected the flexibility of the tunnel in the transverse direction. The findings offer significant new information in the behavior of segmented bored tunnels to guide their future implementation in civil engineering applications.

Reliability and criterion-related validity with a smartphone used in timed-up-and-go test

Background The capacity to diagnosys, quantify and evaluate movement beyond the general confines of a clinical environment under effectiveness conditions may alleviate rampant strain on limited, expensive and highly specialized medical resources. An iPhone 4® mounted a three dimensional accelerometer subsystem with highly robust software applications. The present study aimed to evaluate the reliability and concurrent criterion-related validity of the accelerations with an iPhone 4® in an Extended Timed Get Up and Go test. Extended Timed Get Up and Go is a clinical test with that the patient get up from the chair and walking ten meters, turn and coming back to the chair. Methods A repeated measure, cross-sectional, analytical study. Test-retest reliability of the kinematic measurements of the iPhone 4® compared with a standard validated laboratory device. We calculated the Coefficient of Multiple Correlation between the two sensors acceleration signal of each subject, in each sub-stage, in each of the three Extended Timed Get Up and Go test trials. To investigate statistical agreement between the two sensors we used the Bland-Altman method. Results With respect to the analysis of the correlation data in the present work, the Coefficient of Multiple Correlation of the five subjects in their triplicated trials were as follows: in sub-phase Sit to Stand the ranged between r = 0.991 to 0.842; in Gait Go, r = 0.967 to 0.852; in Turn, 0.979 to 0.798; in Gait Come, 0.964 to 0.887; and in Turn to Stand to Sit, 0.992 to 0.877. All the correlations between the sensors were significant (p < 0.001). The Bland-Altman plots obtained showed a solid tendency to stay at close to zero, especially on the y and x-axes, during the five phases of the Extended Timed Get Up and Go test. Conclusions The inertial sensor mounted in the iPhone 4® is sufficiently reliable and accurate to evaluate and identify the kinematic patterns in an Extended Timed Get and Go test. While analysis and interpretation of 3D kinematics data continue to be dauntingly complex, the iPhone 4® makes the task of acquiring the data relatively inexpensive and easy to use.

A low-cost attack on branch-based software watermarking schemes

In 2005, Ginger Myles and Hongxia Jin proposed a software watermarking scheme based on converting jump instructions or unconditional branch statements (UBSs) by calls to a fingerprint branch function (FBF) that computes the correct target address of the UBS as a function of the generated fingerprint and integrity check. If the program is tampered with, the fingerprint and integrity checks change and the target address will not be computed correctly. In this paper, we present an attack based on tracking stack pointer modifications to break the scheme and provide implementation details. The key element of the attack is to remove the fingerprint and integrity check generating code from the program after disassociating the target address from the fingerprint and integrity value. Using the debugging tools that give vast control to the attacker to track stack pointer operations, we perform both subtractive and watermark replacement attacks. The major steps in the attack are automated resulting in a fast and low-cost attack.

Using decision trees to understand structure in missing data

Objectives Demonstrate the application of decision trees – classification and regression trees (CARTs), and their cousins, boosted regression trees (BRTs) – to understand structure in missing data. Setting Data taken from employees at three different industry sites in Australia. Participants 7915 observations were included. Materials and Methods The approach was evaluated using an occupational health dataset comprising results of questionnaires, medical tests, and environmental monitoring. Statistical methods included standard statistical tests and the ‘rpart’ and ‘gbm’ packages for CART and BRT analyses, respectively, from the statistical software ‘R’. A simulation study was conducted to explore the capability of decision tree models in describing data with missingness artificially introduced. Results CART and BRT models were effective in highlighting a missingness structure in the data, related to the Type of data (medical or environmental), the site in which it was collected, the number of visits and the presence of extreme values. The simulation study revealed that CART models were able to identify variables and values responsible for inducing missingness. There was greater variation in variable importance for unstructured compared to structured missingness. Discussion Both CART and BRT models were effective in describing structural missingness in data. CART models may be preferred over BRT models for exploratory analysis of missing data, and selecting variables important for predicting missingness. BRT models can show how values of other variables influence missingness, which may prove useful for researchers. Conclusion Researchers are encouraged to use CART and BRT models to explore and understand missing data.

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

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/.

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.

Understanding the use of a bug tracking system in a global software development setup

Bug fixing is a highly cooperative work activity where developers, testers, product managers and other stake-holders collaborate using a bug tracking system. In the context of Global Software Development (GSD), where software development is distributed across different geographical locations, we focus on understanding the role of bug trackers in supporting software bug fixing activities. We carried out a small-scale ethnographic fieldwork in a software product team distributed between Finland and India at a multinational engineering company. Using semi-structured interviews and in-situ observations of 16 bug cases, we show that the bug tracker 1) supported information needs of different stake holder, 2) established common-ground, and 3) reinforced issues related to ownership, performance and power. Consequently, we provide implications for design around these findings.