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

David Jones seeks to exploit top end gap in Australian grocery

While Australia’s supermarkets continue to battle on price, the South African owner of David Jones, Woolworths Holdings, has found a gap in the Australian grocery market and is preparing to exploit it. Reports that the group has appointed Pieter de Wet to overhaul the David Jones food business signals once again the ever-changing face of the Australian food and grocery landscape. A re-energised David Jones food offer will provide positive outcomes for both shoppers and suppliers, while potentially becoming another headache for Coles and Woolworths.

Administrative Placement of the Information Systems Discipline in Universities - A SWOT Analysis of Queensland University of Technology

In some Queensland universities, Information Systems academics have moved out of Business Faculties. This study uses a pilot SWOT analysis to examine the ramifications of Information Systems academics being located within or outside of the Business Faculty. The analysis provides a useful basis for decision makers in the School studied, to exploit opportunities and minimise external threats. For Information Systems academics contemplating administrative relocation of their group, the study also offers useful insights. The study presages a series of further SWOT analyses to provide a range of perspectives on the relative merits of having Information Systems academics administratively located inside versus outside Business faculties.

Protocol engineering for protection against denial-of-service attacks

Denial-of-service attacks (DoS) and distributed denial-of-service attacks (DDoS) attempt to temporarily disrupt users or computer resources to cause service un- availability to legitimate users in the internetworking system. The most common type of DoS attack occurs when adversaries °ood a large amount of bogus data to interfere or disrupt the service on the server. The attack can be either a single-source attack, which originates at only one host, or a multi-source attack, in which multiple hosts coordinate to °ood a large number of packets to the server. Cryptographic mechanisms in authentication schemes are an example ap- proach to help the server to validate malicious tra±c. Since authentication in key establishment protocols requires the veri¯er to spend some resources before successfully detecting the bogus messages, adversaries might be able to exploit this °aw to mount an attack to overwhelm the server resources. The attacker is able to perform this kind of attack because many key establishment protocols incorporate strong authentication at the beginning phase before they can iden- tify the attacks. This is an example of DoS threats in most key establishment protocols because they have been implemented to support con¯dentiality and data integrity, but do not carefully consider other security objectives, such as availability. The main objective of this research is to design denial-of-service resistant mechanisms in key establishment protocols. In particular, we focus on the design of cryptographic protocols related to key establishment protocols that implement client puzzles to protect the server against resource exhaustion attacks. Another objective is to extend formal analysis techniques to include DoS- resistance. Basically, the formal analysis approach is used not only to analyse and verify the security of a cryptographic scheme carefully but also to help in the design stage of new protocols with a high level of security guarantee. In this research, we focus on an analysis technique of Meadows' cost-based framework, and we implement DoS-resistant model using Coloured Petri Nets. Meadows' cost-based framework is directly proposed to assess denial-of-service vulnerabil- ities in the cryptographic protocols using mathematical proof, while Coloured Petri Nets is used to model and verify the communication protocols using inter- active simulations. In addition, Coloured Petri Nets are able to help the protocol designer to clarify and reduce some inconsistency of the protocol speci¯cation. Therefore, the second objective of this research is to explore vulnerabilities in existing DoS-resistant protocols, as well as extend a formal analysis approach to our new framework for improving DoS-resistance and evaluating the performance of the new proposed mechanism. In summary, the speci¯c outcomes of this research include following results; 1. A taxonomy of denial-of-service resistant strategies and techniques used in key establishment protocols; 2. A critical analysis of existing DoS-resistant key exchange and key estab- lishment protocols; 3. An implementation of Meadows's cost-based framework using Coloured Petri Nets for modelling and evaluating DoS-resistant protocols; and 4. A development of new e±cient and practical DoS-resistant mechanisms to improve the resistance to denial-of-service attacks in key establishment protocols.

A bridging transition technique for the combination of meshfree method with finite element method in 2D solids and structures

For certain continuum problems, it is desirable and beneficial to combine two different methods together in order to exploit their advantages while evading their disadvantages. In this paper, a bridging transition algorithm is developed for the combination of the meshfree method (MM) with the finite element method (FEM). In this coupled method, the meshfree method is used in the sub-domain where the MM is required to obtain high accuracy, and the finite element method is employed in other sub-domains where FEM is required to improve the computational efficiency. The MM domain and the FEM domain are connected by a transition (bridging) region. A modified variational formulation and the Lagrange multiplier method are used to ensure the compatibility of displacements and their gradients. To improve the computational efficiency and reduce the meshing cost in the transition region, regularly distributed transition particles, which are independent of either the meshfree nodes or the FE nodes, can be inserted into the transition region. The newly developed coupled method is applied to the stress analysis of 2D solids and structures in order to investigate its’ performance and study parameters. Numerical results show that the present coupled method is convergent, accurate and stable. The coupled method has a promising potential for practical applications, because it can take advantages of both the meshfree method and FEM when overcome their shortcomings.

Sleeper [for laptop computer and live performer]

Sleeper is an 18'00" musical work for live performer and laptop computer which exists as both a live performance work and a recorded work for audio CD. The work has been presented at a range of international performance events and survey exhibitions. These include the 2003 International Computer Music Conference (Singapore) where it was selected for CD publication, Variable Resistance (San Francisco Museum of Modern Art, USA), and i.audio, a survey of experimental sound at the Performance Space, Sydney. The source sound materials are drawn from field recordings made in acoustically resonant spaces in the Australian urban environment, amplified and acoustic instruments, radio signals, and sound synthesis procedures. The processing techniques blur the boundaries between, and exploit, the perceptual ambiguities of de-contextualised and processed sound. The work thus challenges the arbitrary distinctions between sound, noise and music and attempts to reveal the inherent musicality in so-called non-musical materials via digitally re-processed location audio. Thematically the work investigates Paul Virilio’s theory that technology ‘collapses space’ via the relationship of technology to speed. Technically this is explored through the design of a music composition process that draws upon spatially and temporally dispersed sound materials treated using digital audio processing technologies. One of the contributions to knowledge in this work is a demonstration of how disparate materials may be employed within a compositional process to produce music through the establishment of musically meaningful morphological, spectral and pitch relationships. This is achieved through the design of novel digital audio processing networks and a software performance interface. The work explores, tests and extends the music perception theories of ‘reduced listening’ (Schaeffer, 1967) and ‘surrogacy’ (Smalley, 1997), by demonstrating how, through specific audio processing techniques, sounds may shifted away from ‘causal’ listening contexts towards abstract aesthetic listening contexts. In doing so, it demonstrates how various time and frequency domain processing techniques may be used to achieve this shift.

Open Specification for BIM : Sydney Opera House Case Study

Executive Summary The objective of this report was to use the Sydney Opera House as a case study of the application of Building Information Modelling (BIM). The Sydney opera House is a complex, large building with very irregular building configuration, that makes it a challenging test. A number of key concerns are evident at SOH: • the building structure is complex, and building service systems - already the major cost of ongoing maintenance - are undergoing technology change, with new computer based services becoming increasingly important. • the current “documentation” of the facility is comprised of several independent systems, some overlapping and is inadequate to service current and future services required • the building has reached a milestone age in terms of the condition and maintainability of key public areas and service systems, functionality of spaces and longer term strategic management. • many business functions such as space or event management require up-to-date information of the facility that are currently inadequately delivered, expensive and time consuming to update and deliver to customers. • major building upgrades are being planned that will put considerable strain on existing Facilities Portfolio services, and their capacity to manage them effectively While some of these concerns are unique to the House, many will be common to larger commercial and institutional portfolios. The work described here supported a complementary task which sought to identify if a building information model – an integrated building database – could be created, that would support asset & facility management functions (see Sydney Opera House – FM Exemplar Project, Report Number: 2005-001-C-4 Building Information Modelling for FM at Sydney Opera House), a business strategy that has been well demonstrated. The development of the BIMSS - Open Specification for BIM has been surprisingly straightforward. The lack of technical difficulties in converting the House’s existing conventions and standards to the new model based environment can be related to three key factors: • SOH Facilities Portfolio – the internal group responsible for asset and facility management - have already well established building and documentation policies in place. The setting and adherence to well thought out operational standards has been based on the need to create an environment that is understood by all users and that addresses the major business needs of the House. • The second factor is the nature of the IFC Model Specification used to define the BIM protocol. The IFC standard is based on building practice and nomenclature, widely used in the construction industries across the globe. For example the nomenclature of building parts – eg ifcWall, corresponds to our normal terminology, but extends the traditional drawing environment currently used for design and documentation. This demonstrates that the international IFC model accurately represents local practice for building data representation and management. • a BIM environment sets up opportunities for innovative processes that can exploit the rich data in the model and improve services and functions for the House: for example several high-level processes have been identified that could benefit from standardized Building Information Models such as maintenance processes using engineering data, business processes using scheduling, venue access, security data and benchmarking processes using building performance data. The new technology matches business needs for current and new services. The adoption of IFC compliant applications opens the way forward for shared building model collaboration and new processes, a significant new focus of the BIM standards. In summary, SOH current building standards have been successfully drafted for a BIM environment and are confidently expected to be fully developed when BIM is adopted operationally by SOH. These BIM standards and their application to the Opera House are intended as a template for other organisations to adopt for the own procurement and facility management activities. Appendices provide an overview of the IFC Integrated Object Model and an understanding IFC Model Data.

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.

Produsage and business : sharing your brand with users

Relations between brands and their users continue to be affected by a traditional perspective that sees the producers and consumers of goods and services as inherently different animals. In the emerging information and knowledge economy, and especially in online contexts, this model is no longer sustainable. Instead, spearheaded by the Web 2.0 phenomenon, there is a trend towards the fusing of production and usage as a new, hybrid process of produsage. This presentation presents the key characteristics driving produsage processes, and describes four guiding principles for businesses as they share their brand with users: * Be open. * Seed community processes by providing content and tools. * Support community dynamics and devolve responsibilities. * Don't exploit the community and its work.

Workflow simulation for operational decision support

Simulation is widely used as a tool for analyzing business processes but is mostly focused on examining abstract steady-state situations. Such analyses are helpful for the initial design of a business process but are less suitable for operational decision making and continuous improvement. Here we describe a simulation system for operational decision support in the context of workflow management. To do this we exploit not only the workflow’s design, but also use logged data describing the system’s observed historic behavior, and incorporate information extracted about the current state of the workflow. Making use of actual data capturing the current state and historic information allows our simulations to accurately predict potential near-future behaviors for different scenarios. The approach is supported by a practical toolset which combines and extends the workflow management system YAWL and the process mining framework ProM.

Unleashing creative writers : situated engagement with mobile narratives

The emergence of sophisticated multimedia phones in combination with improvements to the mobile Internet provides the possibility to read texts and stories on mobile handsets. However, the question is, how to adapt stories in order to take advantage of the user’s mobility and create an engaging and appealing experience. To address these new conditions, a Mobile Narrative was created and access to individual chapters of the story was restricted. Authors can specify constraints, such as a location or time, which need to be met by the reader if they want to read the story. This concept allows creative writers of the story to exploit the fact that the reader’s context is known, by intensifying the user experience and integrating this knowledge into the writing process. Interviews with authors and creative writers and two user studies explored the effects of this way of writing on both parties. The paper presents our preliminary research findings discussing this new experience that was found to be exciting and interesting by both sides.

Mid-level concept learning with visual contextual ontologies and probabilistic inference for image annotation

To date, automatic recognition of semantic information such as salient objects and mid-level concepts from images is a challenging task. Since real-world objects tend to exist in a context within their environment, the computer vision researchers have increasingly incorporated contextual information for improving object recognition. In this paper, we present a method to build a visual contextual ontology from salient objects descriptions for image annotation. The ontologies include not only partOf/kindOf relations, but also spatial and co-occurrence relations. A two-step image annotation algorithm is also proposed based on ontology relations and probabilistic inference. Different from most of the existing work, we specially exploit how to combine representation of ontology, contextual knowledge and probabilistic inference. The experiments show that image annotation results are improved in the LabelMe dataset.

Implementation of an integrated, technology-based, discovery mode assessment item involving an incubation period to enhance learning outcomes for engineering maths students

In this paper we discuss our current efforts to develop and implement an exploratory, discovery mode assessment item into the total learning and assessment profile for a target group of about 100 second level engineering mathematics students. The assessment item under development is composed of 2 parts, namely, a set of "pre-lab" homework problems (which focus on relevant prior mathematical knowledge, concepts and skills), and complementary computing laboratory exercises which are undertaken within a fixed (1 hour) time frame. In particular, the computing exercises exploit the algebraic manipulation and visualisation capabilities of the symbolic algebra package MAPLE, with the aim of promoting understanding of certain mathematical concepts and skills via visual and intuitive reasoning, rather than a formal or rigorous approach. The assessment task we are developing is aimed at providing students with a significant learning experience, in addition to providing feedback on their individual knowledge and skills. To this end, a noteworthy feature of the scheme is that marks awarded for the laboratory work are primarily based on the extent to which reflective, critical thinking is demonstrated, rather than the amount of CBE-style tasks completed by the student within the allowed time. With regard to student learning outcomes, a novel and potentially critical feature of our scheme is that the assessment task is designed to be intimately linked to the overall course content, in that it aims to introduce important concepts and skills (via individual student exploration) which will be revisited somewhat later in the pedagogically more restrictive formal lecture component of the course (typically a large group plenary format). Furthermore, the time delay involved, or "incubation period", is also a deliberate design feature: it is intended to allow students the opportunity to undergo potentially important internal re-adjustments in their understanding, before being exposed to lectures on related course content which are invariably delivered in a more condensed, formal and mathematically rigorous manner. In our presentation, we will discuss in more detail our motivation and rationale for trailing such a scheme for the targeted student group. Some of the advantages and disadvantages of our approach (as we perceived them at the initial stages) will also be enumerated. In a companion paper, the theoretical framework for our approach will be more fully elaborated, and measures of student learning outcomes (as obtained from eg. student provided feedback) will be discussed.

Building information modelling : an issue of adoption and change management

Building Information Modelling (BIM) is an IT enabled technology that allows storage, management, sharing, access, update and use of all the data relevant to a project through out the project life-cycle in the form of a data repository. BIM enables improved inter-disciplinary collaboration across distributed teams, intelligent documentation and information retrieval, greater consistency in building data, better conflict detection and enhanced facilities management. While the technology itself may not be new, and similar approaches have been in use in some other sectors like Aircraft and Automobile industry for well over a decade now, the AEC/FM (Architecture, Engineering and Construction/ Facilities Management) industry is still to catch up with them in its ability to exploit the benefits of the IT revolution. Though the potential benefits of the technology in terms of knowledge sharing, project management, project co-ordination and collaboration are near to obvious, the adoption rate has been rather lethargic, inspite of some well directed efforts and availability of supporting commercial tools. Since the technology itself has been well tested over the years in some other domains the plausible causes must be rooted well beyond the explanation of the ‘Bell Curve of innovation adoption’. This paper discusses the preliminary findings of an ongoing research project funded by the Cooperative Research Centre for Construction Innovation (CRC-CI) which aims to identify these gaps and come up with specifications and guidelines to enable greater adoption of the BIM approach in practice. A detailed literature review is conducted that looks at some of the similar research reported in the recent years. A desktop audit of some of the existing commercial tools that support BIM application has been conducted to identify the technological issues and concerns, and a workshop was organized with industry partners and various players in the AEC industry for needs analysis, expectations and feedback on the possible deterrents and inhibitions surrounding the BIM adoption.

How do other people influence your driving speed? Exploring the 'who' and the 'how' of social influences on speeding from a qualitative perspective

Using only legal sanctions to manage the speed at which people drive ignores the potential benefits of harnessing social factors such as the influence of others. Social influences on driver speeds were explored in this qualitative examination of 67 Australian drivers. Focus group interviews with 8 driver types (young, mid-age and older males and females, and self-identified Excessive and Rare speeders) were guided by Akers’ social learning theory (Akers, 1998). Findings revealed two types of influential others: people known to the driver (passengers and parents), and unknown other drivers. Passengers were generally described as having a slowing influence on drivers: responsibility for the safety of people in the car and consideration for passenger comfort were key themes. In contrast, all but the Rare speeders reported increasing their speed when driving alone. Parental role modelling was also described. In relation to other drivers, key themes included speeding to keep up with traffic flow and perceived pressure to drive faster. This ‘pressure’ from others to ‘speed up’ was expressed in all groups and reported strategies for managing this varied. Encouragingly, examples of actual or anticipated social rewards for speeding were less common than examples of social punishments. Three main themes relating to social punishments were embarrassment, breaching the trust of others, and presenting an image of a responsible driver. Impression management and self-presentation are discussed in light of these findings. Overall, our findings indicate scope to exploit the use of social sanctions for speeding and social praise for speed limit compliance to enhance speed management strategies.