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.

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.

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.

A phenomenological explication of dream interpretation among rural and urban Nguni people

Psychologists investigating dreams in non-Western cultures have generally not considered the meanings of dreams within the unique meaning-structure of the person in his or her societal context. The majority of dream studies in African societies are no exception. Researchers approaching dreams within rural Xhosa and Zulu speaking societies have either adopted an anthropological or a psychodynamic orientation. The latter approach particularly imposes a Western perspective in the interpretation of dream material. There have been no comparable studies of dream interpretation among urban blacks participating in the African Independent Church Movement. The present study focuses on the rural Xhosa speaking people and the urban black population who speak one of the Nguni languages and identify with the African Independent Church Movement. The study is concerned with understanding the meanings of dreams within the cultural context in which they occur. The specific aims of the study are: 1. To explicate the indigenous system of dream interpretation as revealed by acknowledged dream experts. 2. To examine the commonalities and the differences between the interpretation of dreams in two groups, drawn from a rural and urban setting respectively. 3. To elaborate upon the life-world of the participants by the interpretations gained from the above investigation. One hundred dreams and interpretations are collected from two categories of participants referred to as the Rural Group and the Urban Group. The Rural Group is made up of amagqira [traditional healers] and their clients, while the Urban Group consists of prophets and members of the African Independent Churches. Each group includes acknowledged dream experts. A phenomenological methodology is adopted in explicating the data. The methodological precedure involves a number of rigorous stages of expl ication whereby the original data is reduced to Constituent Profiles leading to the construction of a Thematic Index File. By searching and reflect ing upon the data, interpretative themes are identified. These themes are explicated to provide a rigorous description of the interpretative-reality of each group. Themes explicated w i thin the Rural Group are: the physiognomy of the dreamer's life-world as revealed by ithongo, the interpretation of ithongo as revealed through action, the dream relationship as an anticipatory mode-of-existence, iphupha as disclosing a vulnerable mode-of-being, human bodiliness as revealed in dream interpretations and the legitimation of the interpretative-reality within the life-world. Themes explicated within the Urban Group are: the phys iognomy of the dreamer's life-world revealed in their dream-existence, the interpretative-reality revealed through the enaction of dreams, tension between the newer Christian-based cosomology and the traditional cultural-based cosmology, a moral imperative, prophetic perception and human bodiliness, as revealed in dream interpretations and the legitimation of the interpretative-reality within the life-world. The essence of the interpretative-reality of both groups is very similar and is expressed in the notion of relatedness to a cosmic mode-of-being. The cosmic mode-of-being includes a numinous dimension which is expressed through divine presence in the form of ancestors, Holy Spirit or God. These notions cannot be apprehended by theoretical constructs alone but may be grasped and given form in meaning-disclosing intuitions which are expressed in the lifeworld in terms of bodiliness, revelatory knowledge, action and healing. Some differences b e tween the two groups are evident and reveal some conflict between the monotheistic Christian cosmology and the traditional cosmology. Unique aspects of the interpetative-reality of the Urban Group are expressed in terms of difficulties in the urban social environment and the notion of a moral imperative. It is observed that cul tural self-expression based upon traditional ideas continues to play a significant role in the urban environment. The apparent conflict revealed between the respective cosmologies underlies an integration of the aditional meanings with Christian concepts. This finding is consistent with the literature suggesting that the African Independent Church is a syncretic movement. The life-world is based upon the immediate and vivid experience of the numinous as revealed in the dream phenomenon. The participants' approach to dreams is not based upon an explicit theory, but upon an immediate and pathic understanding of the dream phenomenon. The understanding is based upon the interpreter's concrete understanding of the life-world, which includes the possibility of cosmic integration and continuity between the personal and transpersonal realms of being. The approach is characterized as an expression of man's primordial attunement with the cosmos. The approach of the participants to dreams may not b e consistent with a Western rational orientation, but neverthele ss, it is a valid approach . The validity is based upon the immediate life-world of experience which is intelligible, coherent, and above all, it is meaning-giving in revealing life-possibility within the context of human existence.

Harnessing assessment and feedback in the first year to support learning success, engagement and retention

It has been argued that intentional first year curriculum design has a critical role to play in enhancing first year student engagement, success and retention (Kift, 2008). A fundamental first year curriculum objective should be to assist students to make the successful transition to assessment in higher education. Scott (2006) has identified that ‘relevant, consistent and integrated assessment … [with] prompt and constructive feedback’ are particularly relevant to student retention generally; while Nicol (2007) suggests that ‘lack of clarity regarding expectations in the first year, low levels of teacher feedback and poor motivation’ are key issues in the first year. At the very minimum, if we expect first year students to become independent and self-managing learners, they need to be supported in their early development and acquisition of tertiary assessment literacies (Orrell, 2005). Critical to this attainment is the necessity to alleviate early anxieties around assessment information, instructions, guidance, and performance. This includes, for example:  inducting students thoroughly into the academic languages and assessment genres they will encounter as the vehicles for evidencing learning success; and  making expectations about the quality of this evidence clear. Most importantly, students should receive regular formative feedback of their work early in their program of study to aid their learning and to provide information to both students and teachers on progress and achievement. Leveraging research conducted under an ALTC Senior Fellowship that has sought to articulate a research-based 'transition pedagogy' (Kift & Nelson, 2005) – a guiding philosophy for intentional first year curriculum design and support that carefully scaffolds and mediates the first year learning experience for contemporary heterogeneous cohorts – this paper will discuss theoretical and practical strategies and examples that should be of assistance in implementing good assessment and feedback practices across a range of disciplines in the first year.

Designing for engagement : building IT systems

Context The School of Information Technology at QUT has recently undertaken a major restructuring of their Bachelor of Information Technology (BIT) course. Some of the aims of this restructuring include a reduction in first year attrition and to provide an attractive degree course that meets both student and industry expectations. Emphasis has been placed on the first semester in the context of retaining students by introducing a set of four units that complement one another and provide introductory material on technology, programming and related skills, and generic skills that will aid the students throughout their undergraduate course and in their careers. This discussion relates to one of these four fist semester units, namely Building IT Systems. The aim of this unit is to create small Information Technology (IT) systems that use programming or scripting, databases as either standalone applications or web applications. In the prior history of teaching introductory computer programming at QUT, programming has been taught as a stand alone subject and integration of computer applications with other systems such as databases and networks was not undertaken until students had been given a thorough grounding in those topics as well. Feedback has indicated that students do not believe that working with a database requires programming skills. In fact, the teaching of the building blocks of computer applications have been compartmentalized and taught in isolation from each other. The teaching of introductory computer programming has been an industry requirement of IT degree courses as many jobs require at least some knowledge of the topic. Yet, computer programming is not a skill that all students have equal capabilities of learning (Bruce et al., 2004) and this is clearly shown by the volume of publications dedicated to this topic in the literature over a broad period of time (Eckerdal & Berglund, 2005; Mayer, 1981; Winslow, 1996). The teaching of this introductory material has been done pretty much the same way over the past thirty years. During this period of time that introductory computer programming courses have been taught at QUT, a number of different programming languages and programming paradigms have been used and different approaches to teaching and learning have been attempted in an effort to find the golden thread that would allow students to learn this complex topic. Unfortunately, computer programming is not a skill that can be learnt in one semester. Some basics can be learnt but it can take many years to master (Norvig, 2001). Faculty data typically has shown a bimodal distribution of results for students undertaking introductory programming courses with a high proportion of students receiving a high mark and a high proportion of students receiving a low or failing mark. This indicates that there are students who understand and excel with the introductory material while there is another group who struggle to understand the concepts and practices required to be able to translate a specification or problem statement into a computer program that achieves what is being requested. The consequence of a large group of students failing the introductory programming course has been a high level of attrition amongst first year students. This attrition level does not provide good continuity in student numbers in later years of the degree program and the current approach is not seen as sustainable.