Supplementary Information : Hogan, Holland, Holloway, Petit and Read : Read Classification for Next Generation Sequencing, ESANN 2013, April 2013

This item provides supplementary materials for the paper mentioned in the title, specifically a range of organisms used in the study. The full abstract for the main paper is as follows: Next Generation Sequencing (NGS) technologies have revolutionised molecular biology, allowing clinical sequencing to become a matter of routine. NGS data sets consist of short sequence reads obtained from the machine, given context and meaning through downstream assembly and annotation. For these techniques to operate successfully, the collected reads must be consistent with the assumed species or species group, and not corrupted in some way. The common bacterium Staphylococcus aureus may cause severe and life-threatening infections in humans,with some strains exhibiting antibiotic resistance. In this paper, we apply an SVM classifier to the important problem of distinguishing S. aureus sequencing projects from alternative pathogens, including closely related Staphylococci. Using a sequence k-mer representation, we achieve precision and recall above 95%, implicating features with important functional associations.

On the zeros of the Abelian integrals for a class of Liénard systems

A planar polynomial differential system has a finite number of limit cycles. However, finding the upper bound of the number of limit cycles is an open problem for the general nonlinear dynamical systems. In this paper, we investigated a class of Liénard systems of the form x'=y, y'=f(x)+y g(x) with deg f=5 and deg g=4. We proved that the related elliptic integrals of the Liénard systems have at most three zeros including multiple zeros, which implies that the number of limit cycles bifurcated from the periodic orbits of the unperturbed system is less than or equal to 3.

Experiences with an Object-Oriented, Multi-Stage Language

Metaphor is a multi-stage programming language extension to an imperative, object-oriented language in the style of C# or Java. This paper discusses some issues we faced when applying multi-stage language design concepts to an imperative base language and run-time environment. The issues range from dealing with pervasive references and open code to garbage collection and implementing cross-stage persistence.

Task profiling : A task-Based approach to measuring the integration of ICT in the classroom

The measurement of ICT (information and communication technology) integration is emerging as an area of research interest with such systems as Education Queensland including it in their recently released list of research priorities. Studies to trial differing integration measurement instruments have taken place within Australia in the last few years, particularly Western Australia (Trinidad, Clarkson, & Newhouse, 2004; Trinidad, Newhouse & Clarkson, 2005), Tasmania (Fitzallen 2005) and Queensland (Finger, Proctor, & Watson, 2005). This paper will add to these investigations by describing an alternate and original methodological approach which was trialled in a small-scale pilot study conducted jointly by Queensland Catholic Education Commission (QCEC) and the Centre of Learning Innovation, Queensland University of Technology (QUT) in late 2005. The methodology described is based on tasks which, through a process of profiling, can be seen to be artefacts which embody the internal and external factors enabling and constraining ICT integration.

Final report implementation of relational management

Construction teams and construction organisations have their own distinctive cultures. There also exists an infrastructure, both social and contractual, which ensures that these projects within which the teams operate are completed successfully. It is these issues which this research has addressed. The project was instigated by Queensland Department of Main Roads, Public Works and John Holland Group in order to address how they might better implement relationship management (RM) on their construction projects. The project was devised initially in order to facilitate a change in culture which would allow the project to be run in a relational manner and would lead to effective performance in terms of the KPIs that the organisations set for themselves, described as business better than usual. This report describes the project, its outcomes and deliverable and indicates the changes that were made to the project during the research process. Hence, the initial premise of the project and the problem to investigate was the implementation of relational contracting: • throughout a range of projects; • with a focus on client body staff. The additions that were made to the project, and documented in the variations to the project, included two major additional areas of study: • client management and stakeholder management; • a live case study of an alliancing project. The context within which the research was undertaken is important. The research was driven by main roads with their desire to improve their operations by focusing on the relationship between the major project participants (however, stakeholder and client organisation management became an obvious issue as the research progressed, hence the variations). The context was initially focussed on main roads, public works and John Holland group organisations but it became clear very quickly that this was in fact an industry-wide issue and not an issue specific solely to the project participants. Hence, the context within which this research took place can be described as below: The deliverables from the project are a toolkit for determining RM needs in an organisation, a monograph describing the practical implementation of RM and the outline for a RM CPD and Masters course

Managing infrastructure transitions : a complex adaptive systems perspective

Engineering assets such as roads, rail, bridges and other forms of public works are vital to the effective functioning of societies {Herder, 2006 #128}. Proficient provision of this physical infrastructure is therefore one of the key activities of government {Lædre, 2006 #123}. In order to ensure engineering assets are procured and maintained on behalf of citizens, government needs to devise the appropriate policy and institutional architecture for this purpose. The changing institutional arrangements around the procurement of engineering assets are the focus of this paper. The paper describes and analyses the transition to new, more collaborative forms of procurement arrangements which are becoming increasingly prevalent in Australia and other OECD countries. Such fundamental shifts from competitive to more collaborative approaches to project governance can be viewed as a major transition in procurement system arrangements. In many ways such changes mirror the shift from New Public Management, with its emphasis on the use of market mechanisms to achieve efficiencies {Hood, 1991 #166}, towards more collaborative approaches to service delivery, such as those under network governance arrangements {Keast, 2007 #925}. However, just as traditional forms of procurement in a market context resulted in unexpected outcomes for industry, such as a fragmented industry afflicted by chronic litigation {Dubois, 2002 #9}, the change to more collaborative forms of procurement is unlikely to be a panacea to the problems of procurement, and may well also have unintended consequences. This paper argues that perspectives from complex adaptive systems (CAS) theory can contribute to the theory and practice of managing system transitions. In particular the concept of emergence provides a key theoretical construct to understand the aggregate effect that individual project governance arrangements can have upon the structure of specific industries, which in turn impact individual projects. Emergence is understood here as the macro structure that emerges out of the interaction of agents in the system {Holland, 1998 #100; Tang, 2006 #51}.

Sustainable transport and the impact on the built environment : Future trends and directions

We love the automobile and the independence that it gives us. We are more mobile than we have ever been before in recorded history. In Australia 80% of journeys are by private motor vehicle. But it is becoming increasingly obvious that this era has a very limited lifespan. Fuel prices have skyrocketed recently with no end in sight. In spite of massive amounts of road construction, our cities are becoming increasingly congested. We desperately need to address climate change and the automobile is a major contributor. Carbon trading schemes will put even more upward pressure on fuel prices. At some point in the near future, most of us will need to reconsider our automobile usage whether we like it or not. The time to plan for the future is now. But what will happen to our mobility when access to cheap and available petroleum becomes a thing of the past? Will we start driving electric/hydrogen/ethanol vehicles? Or will we flock to public transport? Will our public transport systems cope with a massive increase in demand? Will thousands of people take to alternatives such as bicycles? If so, where do we put them? How do we change our roads to cope? How do we change our buildings to suit? Will we need recharging stations in our car park for example? Some countries are less reliant on the car than others e.g. Holland and Germany. How can the rest of the world learn from them? This paper discusses many of the likely outcomes of the inevitable shift away from society’s reliance on petroleum and examines the expected impact on the built environment. It also looks at ways in which the built environment can be planned to help ease the transition to a fossil free world. 1.

Information–movement coupling in developing cricketers under changing ecological practice constraints

Changing informational constraints of practice, such as when using ball projection machines, has been shown to significantly affect movement coordination of skilled cricketers. To date, there has been no similar research on movement responses of developing batters, an important issue since ball projection machines are used heavily in cricket development programmes. Timing and coordination of young cricketers (n = 12, age = 15.6 ± 0.7 years) were analyzed during the forward defensive and forward drive strokes when facing a bowling machine and bowler (both with a delivery velocity of 28.14 ± 0.56 m s−1). Significant group performance differences were observed between the practice task constraints, with earlier initiation of the backswing, front foot movement, downswing, and front foot placement when facing the bowler compared to the bowling machine. Peak height of the backswing was higher when facing the bowler, along with a significantly larger step length. Altering the informational constraints of practice caused major changes to the information–movement couplings of developing cricketers. Data from this study were interpreted to emanate from differences in available specifying variables under the distinct practice task constraints. Considered with previous findings, results confirmed the need to ensure representative batting task constraints in practice, cautioning against an over-reliance on ball projection machines in cricket development programmes.