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.

The role of decision-maker preferences in tenancy selection of CBD office accommodation – preliminary literature review

The literature and anecdotal evidence suggests that that there is more to tenancy selection (firm location) than the profit maximisation drive that traditional neo-classical economic location theory suggests. In the first instance these models assume property markets are rational and perfectly competitive; the CBD office market is clearly neither rational nor perfectly competitive. This fact alone relegates such models to the margins of usefulness for an industry that seeks to satisfy tenant demand in order to optimise returns on capital invested. Acknowledgment of property market imperfections are universally accepted to the extent that all contemporary texts discuss the lack of a coherent centralised market place and incomplete and poorly disseminated information processes as fundamental inadequacies which characterise the property market inefficiencies. Less well researched are the facets of the market which allow the observer to determine market activity to be significantly irrational. One such facet is that of ‘decision maker preferences’. The decision to locate a business operation at one location as opposed to another seems ostensibly a routine choice based on short, medium and long term business objectives. These objectives are derived from a process of strategic planning by one or more individuals whose goal is held to be to optimise outcomes which benefit the business (and presumably those employed within it). However the decision making processes appear bounded by how firms function, the institutional context in which they operate, as well as by opportunistic behaviour by individual decision makers who allow personal preferences to infiltrate and ‘corrupt’ the process. In this way, history, culture, geography, as well as institutions all become significant to the extent that these influence and shape individual behaviour which in turn determine the morphology of individual preferences, as well as providing a conduit for them to take effect. This paper exams historical and current literature on the impact of individual behaviour in the decision making process within organisations as a precursor to an investigation of the tenancy decision making process within the CBD office market. Literature on the topic falls within a number of research disciplines, philosophy, psychology and economics to name a few.

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.

Further evidence of a relationship between explaining, tracing and writing skills in introductory programming

This paper reports on a replication of earlier studies into a possible hierarchy of programming skills. In this study, the students from whom data was collected were at a university that had not provided data for earlier studies. Also, the students were taught the programming language Python, which had not been used in earlier studies. Thus this study serves as a test of whether the findings in the earlier studies were specific to certain institutions, student cohorts, and programming languages. Also, we used a non–parametric approach to the analysis, rather than the linear approach of earlier studies. Our results are consistent with the earlier studies. We found that students who cannot trace code usually cannot explain code, and also that students who tend to perform reasonably well at code writing tasks have also usually acquired the ability to both trace code and explain code.

Informe

Much landscape architectural form seems like hackneyed modernism, whether it be orthogonal or biomorphic, 'formal or informal' and doesn't seem to get to grips with the truly complex nature of the landscape, making any project seem potentially simplistic. This is largely because it has inherited languages from architecture that are based around objects, and that therefore can act to make designs self-referential rather than edgy instances in a dialogue much larger than the site itself, connected to systems that are unavoidable, even if one chooses to ignore them. These systems constitute a formal language even if landscape architecture looks to things like GIS to engage with them. Tropospheric Temperament was an Advanced Computing subject, for second-year landscape architecture students at UWA, taught by Julian Raxworthy and Rene Van Meeuwen, which ran in Semester 1, 2004. For this subject, the question was: how can we learn to wield such systems in design terms, even if they are developed through un-self-conscious natural and vernacular forces?

Bike park in Groningen, The Netherlands

Groningen is a city that collects contemporary projects. A trip around town reveals something like a zoo, with examples of all design languages of the last twenty years, many of them now aging and distinctly past their prime. Even though some of these projects are outdated, this collection not only demonstrates a commitment to design (even occasionally lacking judgement) but also serves an archival function: we can consult the Groningen Zoo of Design to determine the design to determine the design preoccupations of the past and how those often theoretical interests (since most of the work by these designers was not built) manifested themselves in material form on the ground.

Dancing between diversity and consistency : refining assessment in postgraduate degrees in dance

This publication is the culmination of a 2 year Australian Learning and Teaching Council's Project Priority Programs Research Grant which investigates key issues and challenges in developing flexible guidelines lines for best practice in Australian Doctoral and Masters by Research Examination, encompassing the two modes of investigation, written and multi-modal (practice-led/based) theses, their distinctiveness and their potential interplay. The aims of the project were to address issues of assessment legitimacy raised by the entry of practice-orientated dance studies into Australian higher degrees; examine literal embodiment and presence, as opposed to cultural studies about states of embodiment; foreground the validity of questions around subjectivity and corporeal intelligence/s and the reliability of artistic/aesthetic communications, and finally to celebrate ‘performance mastery’(Melrose 2003) as a rigorous and legitimate mode of higher research. The project began with questions which centred around: the functions of higher degree dance research; concepts of 'master-ness’ and ‘doctorateness’; the kinds of languages, structures and processes which may guide candidates, supervisors, examiners and research personnel; the purpose of evaluation/examination; addressing positive and negative attributes of examination. Finally the study examined ways in which academic/professional, writing/dancing, tradition/creation and diversity/consistency relationships might be fostered to embrace change. Over two years, the authors undertook a qualitative national study encompassing a triangulation of semi-structured face to face interviews and industry forums to gather views from the profession, together with an analysis of existing guidelines, and recent literature in the field. The most significant primary data emerged from 74 qualitative interviews with supervisors, examiners, research deans and administrators, and candidates in dance and more broadly across the creative arts. Qualitative data gathered from the two primary sources, was coded and analysed using the NVivo software program. Further perspectives were drawn from international consultant and dance researcher Susan Melrose, as well as publications in the field, and initial feedback from a draft document circulated at the World Dance Alliance Global Summit in July 2008 in Brisbane. Refinement of data occurred in a continual sifting process until the final publication was produced. This process resulted in a set of guidelines in the form of a complex dynamic system for both product and process oriented outcomes of multi-modal theses, along with short position papers on issues which arose from the research such as contested definitions, embodiment and ephemerality, ‘liveness’ in performance research higher degrees, dissolving theory/practice binaries, the relationship between academe and industry, documenting practices and a re-consideration of the viva voce.

Ownerships for reasoning about parallelism : type system and semantics

Technical Report to accompany Ownership for Reasoning About Parallelism. Documents type system which captures effects and the operational semantics for the language which is presented as part of the paper.

Detecting and resolving redundancies in EP3P policies

Current regulatory requirements on data privacy make it increasingly important for enterprises to be able to verify and audit their compliance with their privacy policies. Traditionally, a privacy policy is written in a natural language. Such policies inherit the potential ambiguity, inconsistency and mis-interpretation of natural text. Hence, formal languages are emerging to allow a precise specification of enforceable privacy policies that can be verified. The EP3P language is one such formal language. An EP3P privacy policy of an enterprise consists of many rules. Given the semantics of the language, there may exist some rules in the ruleset which can never be used, these rules are referred to as redundant rules. Redundancies adversely affect privacy policies in several ways. Firstly, redundant rules reduce the efficiency of operations on privacy policies. Secondly, they may misdirect the policy auditor when determining the outcome of a policy. Therefore, in order to address these deficiencies it is important to identify and resolve redundancies. This thesis introduces the concept of minimal privacy policy - a policy that is free of redundancy. The essential component for maintaining the minimality of privacy policies is to determine the effects of the rules on each other. Hence, redundancy detection and resolution frameworks are proposed. Pair-wise redundancy detection is the central concept in these frameworks and it suggests a pair-wise comparison of the rules in order to detect redundancies. In addition, the thesis introduces a policy management tool that assists policy auditors in performing several operations on an EP3P privacy policy while maintaining its minimality. Formal results comparing alternative notions of redundancy, and how this would affect the tool, are also presented.

Enforcing P3P policies using a digital rights management system

The protection of privacy has gained considerable attention recently. In response to this, new privacy protection systems are being introduced. SITDRM is one such system that protects private data through the enforcement of licenses provided by consumers. Prior to supplying data, data owners are expected to construct a detailed license for the potential data users. A license specifies whom, under what conditions, may have what type of access to the protected data. The specification of a license by a data owner binds the enterprise data handling to the consumer’s privacy preferences. However, licenses are very detailed, may reveal the internal structure of the enterprise and need to be kept synchronous with the enterprise privacy policy. To deal with this, we employ the Platform for Privacy Preferences Language (P3P) to communicate enterprise privacy policies to consumers and enable them to easily construct data licenses. A P3P policy is more abstract than a license, allows data owners to specify the purposes for which data are being collected and directly reflects the privacy policy of an enterprise.

Towards executable specification : combining i* and AgentSpeak(L).

Agent-oriented conceptual modelling (AoCM) approaches in Requirements Engineering (RE) have received considerable attention recently. Semi-formal modeling frameworks such as i* assist analysts in requirements elicitation and reasoning of early-phase RE. AgentSpeak(L) is a widely accepted agent programming language. The Strategic Rationale (SR) model of the i* framework naturally lends itself to AgentSpeak(L) programs. Furthermore, the Strategic Dependency (SD) component of the i* framework prescribes the interaction between the agents in a multi-agent environment. This paper proposes a formal methodology for transforming a SR model to an AgentS- peak(L) agent. The constructed AgentSpeak(L) agents will then form the essential components of a multi-agent system, MAS.

Making sense of the resource-based view?

The Resource Based View (RBV) of strategic management has been criticized for relying on inconsistent assumptions of rationality, and mutually inconsistent underlying hypotheses. In this paper, I outline how these critiques can be addressed by re-building RBV on a sense-making foundation. The core notions from sense-making of bounded cognition, retrospective sense-making, incrementalism, loose coupling, causal maps and organizational paradigm are introduced. These are then used to propose a re-construction of key RBV constructs, extending some conceptual discussions, and providing for a conceptually consistent formulation. Implications for the use of RBV as a theory and future research are discussed.

A study of entrepreneurship : Taiwanese digital content companies in China

China’s accession to the World Trade Organisation (WTO) has greatly enhanced global interest in investment in the Chinese media market, where demand for digital content is growing rapidly. The East Asian region is positioned as a growth area in many forms of digital content and digital service industries. China is attempting to catch up and take its place as a production centre to offset challenges from neighbouring countries. Meanwhile, Taiwan is seeking to use China both as an export market and as a production site for its digital content. This research investigates entry strategies of Taiwanese digital content firms into the Chinese market. By examining the strategies of a sample of Taiwan-based companies, this study also explores the evolution of their market strategies. However, the focus is on how distinctive business practices such as guanxi are important to Taiwanese business and to relations with Mainland China. This research examines how entrepreneurs manage the characteristics of digital content products and in turn how digital content entrepreneurs adapt to changing market circumstances. This project selected five Taiwan-based digital content companies that have business operations in China: Wang Film, Artkey, CnYES, Somode and iPartment. The study involved a field trip, undertaken between November 2006 and March 2007 to Shanghai and Taiwan to conduct interviews and to gather documentation and archival reports. Six senior managers and nine experts were interviewed. Data were analysed according to Miller’s firm-level entrepreneurship theory, foreign direct investment theory, Life Cycle Model and guanxi philosophy. Most studies of SMEs have focused on free market (capitalist) environments. In contrast, this thesis examines how Taiwanese digital content firms’ strategies apply in the Chinese market. I identified three main types of business strategy: cost-reduction, innovation and quality-enhancement; and four categories of functional strategies: product, marketing, resource acquisition and organizational restructuring. In this study, I introduce the concept of ‘entrepreneurial guanxi’, special relationships that imply mutual obligation, assurance and understanding to secure and exchange favors in entrepreneurial activities. While guanxi is a feature of many studies of business in Pan-Chinese society, it plays an important mediating role in digital content industries. In this thesis, I integrate the ‘Life Cycle Model’ with the dynamic concept of strategy. I outline the significant differences in the evolution of strategy between two types of digital content companies: off-line firms (Wang Film and Artkey) and web-based firms (CnYES, Somode and iPartment). Off-line digital content firms tended to adopt ‘resource acquisition strategies’ in their initial stages and ‘marketing strategies’ in second and subsequent stages. In contrast, web-based digital content companies mainly adopted product and marketing strategies in the early stages, and would adopt innovative approaches towards product and marketing strategies in the whole process of their business development. Some web-based digital content companies also adopted organizational restructuring strategies in the final stage. Finally, I propose the ‘Taxonomy Matrix of Entrepreneurial Strategies’ to emphasise the two dimensions of this matrix: innovation, and the firm’s resource acquisition for entrepreneurial strategy. This matrix is divided into four cells: Effective, Bounded, Conservative, and Impoverished.

Getting skilled for education, training and employment : Indigenous Cultural Knowledges and mainstream knowledges of mathematics

This abstract is a preliminary discussion of the importance of blending of Indigenous cultural knowledges with mainstream knowledges of mathematics for supporting Indigenous young people. This import is emphasised in the documents Preparing the Ground for Partnership (Priest, 2005), The Indigenous Education Strategic Directions 2008–2011 (Department of Education, Training and the Arts, 2007) and the National Goals for Indigenous Education (Department of Education, Employment and Work Relations, 2008). These documents highlight the contextualising of literacy and numeracy to students’ community and culture (see Priest, 2005). Here, Community describes “a culture that is oriented primarily towards the needs of the group. Martin Nakata (2007) describes contextualising to culture as about that which already exists, that is, Torres Strait Islander community, cultural context and home languages (Nakata, 2007, p. 2). Continuing, Ezeife (2002) cites Hollins (1996) in stating that Indigenous people belong to “high-context culture groups” (p. 185). That is, “high-context cultures are characterized by a holistic (top-down) approach to information processing in which meaning is “extracted” from the environment and the situation. Low-context cultures use a linear, sequential building block (bottom-up) approach to information processing in which meaning is constructed” (p.185). In this regard, students who use holistic thought processing are more likely to be disadvantaged in mainstream mathematics classrooms. This is because Westernised mathematics is presented as broken into parts with limited connections made between concepts and with the students’ culture. It potentially conflicts with how they learn. If this is to change the curriculum needs to be made more culture-sensitive and community orientated so that students know and understand what they are learning and for what purposes.

Seeing is understanding : the effect of visualisation in understanding programming concepts

How and why visualisations support learning was the subject of this qualitative instrumental collective case study. Five computer programming languages (PHP, Visual Basic, Alice, GameMaker, and RoboLab) supporting differing degrees of visualisation were used as cases to explore the effectiveness of software visualisation to develop fundamental computer programming concepts (sequence, iteration, selection, and modularity). Cognitive theories of visual and auditory processing, cognitive load, and mental models provided a framework in which student cognitive development was tracked and measured by thirty-one 15-17 year old students drawn from a Queensland metropolitan secondary private girls’ school, as active participants in the research. Seventeen findings in three sections increase our understanding of the effects of visualisation on the learning process. The study extended the use of mental model theory to track the learning process, and demonstrated application of student research based metacognitive analysis on individual and peer cognitive development as a means to support research and as an approach to teaching. The findings also forward an explanation for failures in previous software visualisation studies, in particular the study has demonstrated that for the cases examined, where complex concepts are being developed, the mixing of auditory (or text) and visual elements can result in excessive cognitive load and impede learning. This finding provides a framework for selecting the most appropriate instructional programming language based on the cognitive complexity of the concepts under study.