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.

A learning community approach to doctoral education in the social sciences

The paper reports on the findings of a community learning approach to doctoral education involving scholarly writing groups (SWGs) which was developed and implemented in the context of a higher degree research programme within the social sciences in an Australian university. The research evaluated the impact of the teaching intervention on students' perceptions of the community learning experience, their knowledge of scholarly writing and their attitudes towards writing. The findings are suggestive of the advantages of community approaches to learning in higher degree research education as a supplement to independent supervision. The SWGs were associated with improvements in both participants' knowledge of scholarly writing and their attitudes towards writing. However, a variety of characteristics of doctoral education are potential impediments to the creation of ongoing and regular interactions in learning communities such as SWGs. The paper concludes that a flexible approach to the recognition and enhancement of community approaches to learning is required to acknowledge the complex and diverse context of contemporary doctoral education.

Crossing boundaries: Implications of advances in basic sciences for the management of addiction.

This set of papers in this issue of "Addictive Behaviors" was presented at the 2004 'Addictions' conference, which, for the first time, was held in the Southern Hemisphere, on the Sunshine Coast of Queensland, Australia. The theme of the conference, Crossing Boundaries: Implications of Advances in Basic Sciences for the Management of Addiction, speaks for itself. The papers derive from a wide range of empirical paradigms and cover issues with relevance to the development of addiction, to the maintenance of problematic use, and to assessment, treatment, and relapse. Research from Europe and the United States is represented, as well as work from Australia. An international perspective is strongly emphasized from the initial paper by Obot, Poznyak, and Moneiro, (see record 2004-19599-015) which describes the WHO Report on the Neuroscience of Psychoactive Substance Use and Dependence, and summarises some of the report's implications for policy and practice. Hall, Carter, and Morley (see record 2004-19599-014) close the issue with a paper on the wide-ranging ethical implications of advances in neuroscience research, including issues arising from the identification of high risk for addiction, the potential for coercive pharmacotherapy, use of medications to enhance function, and risks to privacy.

Will they know enough? Pre-service primary teachers' knowledge base for teaching intergrated social sciences

A significant issue in primary teacher education is developing a knowledge base which prepares teachers to teach in a range of subject areas. In Australia, the problem in primary social science education is compounded by the integrated nature of the key learning area of Studies of Society and Environment (SOSE). Recent debates on teaching integrated social sciences omit discussions on the knowledge base for teaching. In this paper, a case study approach is used to investigate primary pre-service teachers’ approaches to developing a knowledge base in designing a SOSE curriculum unit. Data from five teacher-educators who taught primary SOSE curriculum indicates that novice teachers’ subject content knowledge, as revealed through their curriculum planning, lacked a disciplinary basis. However, understanding of inquiry learning, which is fundamental to social science education, was much stronger. This paper identifies a gap in the scholarship on teaching integrated social science and illustrates the need to support and develop primary teachers’ disciplinary knowledge in teacher education.

Southern theory : the global dynamics of knowledge in the social sciences

Up front I am impelled to acknowledge an intellectual debt to Raewyn Connell as one of my PhD supervisors about 20 years ago and as having a lasting influence on my own sociological approach to research. One of key themes of this book is that southern theorists are rarely read in the northern hemisphere. This is not the case for Connell, however, one of Australia’s most internationally renowned scholars. The tome reads as the creative outpouring of her lifelong thirst for social science. Its main claim is that southern theory ‘has as much intellectual power as metropolitan social thought, and more political relevance’ (p. xii). A big but compelling claim, as I will explain.

Implicit discount rates and fisheries management : is there a relationship?

Fishers are faced with multiple risks, including unpredictability of future catch rates, prices and costs. While the latter are largely beyond the control of fisheries managers, effective fisheries management should reduce uncertainty about future catches. Different management instruments are likely to have different impacts on the risk perception of fishers, and this should manifest itself in their implicit discount rate. Assuming licence and quota values represent the net present value of the flow of expected future profits, then a proxy for the implicit discount rate of vessels in a fishery can be derived by the ratio of the average level of profits to the average licence/quota value. From this, an indication of the risk perception can be derived, assuming higher discount rates reflect higher levels of systematic risk. In this paper, we apply the capital asset pricing model (CAPM) to determine the risk premium implicit in the discount rates for a range of Australian fisheries, and compare this with the set of management instruments in place. We test the assumption that rights based management instruments lower perceptions of risk in fisheries. We find little evidence to support this assumption. although the analysis was based on only limited data.

Impacts of vessel capacity reduction programs on the efficiency in fisheries. The case of Australia's multispecies in northern prawn fishery

Capacity reduction programs in the form of buybacks or decommissioning programs have had relatively widespread application in fisheries in the US, Europe and Australia. A common criticism of such programs is that they remove the least efficient vessels first, resulting in an increase in average efficiency of the remaining fleet. The effective fishing power of the fleet, therefore, does not decrease in proportion to the number of vessels removed. Further, reduced crowding may increase efficiency of the remaining vessels. In this paper, the effects of a buyback program on average technical efficiency in Australia’s Northern Prawn Fishery are examined using a multi-output distance function approach with an explicit inefficiency model. The results indicate that average efficiency of the remaining vessels was greater than that of the removed vessels, and that average efficiency of remaining vessels also increased as a result of reduced crowding.

Best practices in prediction for decision-making : lessons from the atmospheric and earth sciences

Predictions that result from scientific research hold great appeal for decision-makers who are grappling with complex and controversial environmental issues, by promising to enhance their ability to determine a need for and outcomes of alternative decisions. A problem exists in that decision-makers and scientists in the public and private sectors solicit, produce, and use such predictions with little understanding of their accuracy or utility, and often without systematic evaluation or mechanisms of accountability. In order to contribute to a more effective role for ecological science in support of decision-making, this paper discusses three ``best practices'' for quantitative ecosystem modeling and prediction gleaned from research on modeling, prediction, and decision-making in the atmospheric and earth sciences. The lessons are distilled from a series of case studies and placed into the specific context of examples from ecological science.

Values, wellness and the social sciences curriculum

Recent initiatives in values education in Australia emphasise the importance of the process of valuing and general methodologies that foster this in the classroom. Although a range of strategies are available, this chapter argues that inquiry-based approaches in the Social Sciences play a significant role in linking valuing processes with decision making skills. Collectively, these approaches prompt the development of reasoning and self awareness which also impact on student wellness. This chapter proposes some curriculum approaches to foreground values education in the Australian Social Sciences classroom. It argues that valuing is an important life skill that can be cultivated in the classroom through specific valuing strategies. It contends that the development of the capacity to make informed value choices is a critical factor in promoting wellness and resilience in students and in preparing them for the decision making skills required for effective participation in society.

Embedding values through global education in social sciences pre-service teacher education : linking the head and heart

This chapter aims to situate values education as a core component of social science pre-service teacher education. In particular, it reflects on an experiment in embedding a values laden Global Education perspective in a fourth year social science curriculum method unit. This unit was designed and taught by the researcher on the assumption that beginning social science teachers need to be empowered with pedagogical skills and new dispositions to deal with value laden emerging global and regional concerns in their secondary school classrooms. Moreover, it was assumed that when pre-service teachers engage in dynamic and interactive learning experiences in their curriculum unit, they commence the process of ‘capacity building’ those skills which prepare them for their own lifelong professional learning. This approach to values education also aimed at providing pre-service teachers with opportunities to ‘create deep understandings of teaching and learning’ (Barnes, 1989, p. 17) by reflecting on the ways in which ‘pedagogy can be transformative’ (Lovat and Toomey, 2011 add page no from Chapter One). It was assumed that this tertiary experience would foster the sine qua non of teaching – a commitment to students and their learning. Central to fostering new ‘dispositions’ through this approach, was the belief in the power of pedagogy to make the difference in enhancing student participation and learning. In this sense, this experiment in values education in secondary social science pre-service teacher education aligns with the Troika metaphor for a paradigm change, articulated by Lovat and Toomey (2009) in Chapter One.

Genetic analysis reveals two stocks of skipjack tuna (Katsuwonus pelamis) in the north western Indian Ocean

Skipjack (SJT) (Katsuwonus pelamis) is a medium sized, pelagic, highly dispersive tuna species that occurs widely across tropical and subtropical waters. SJT constitute the largest tuna fishery in the Indian Ocean, and are currently managed as a single stock. Patterns of genetic variation in a mtDNA gene and 6 microsatellite loci were examined to test for stock structure in the northwestern Indian Ocean. 324 individuals were sampled from five major fishing grounds around Sri Lanka, and single sites in the Maldive Islands and the Laccadive Islands. Phylogenetic reconstruction of mtDNA revealed two coexisting divergent clades in the region. AMOVA (Analysis of Molecular Variance) of mtDNA data revealed significant genetic differentiation among sites (ΦST = 0.2029, P < 0.0001), also supported by SAMOVA results. AMOVA of microsatellite data also showed significant differentiation among most sampled sites (FST = 0.0256, P<0.001) consistent with the mtDNA pattern. STRUCTURE analysis of the microsatellite data revealed two differentiated stocks. While the both two marker types examined identified two genetic groups, microsatellite analysis indicates that the sampled SJT are likely to represent individuals sourced from discrete breeding grounds that are mixed in feeding grounds in Sri Lankan waters.

Enhancing the teaching of family and consumer sciences : the role of graphic organisers

In a world of constant and rapid change there are greater demands placed on learners to not only gain content knowledge, but also to develop learning skills and to adopt new strategies that will enable them to produce better and faster learning outcomes. Especially in internationally advancing nations like Kuwait this will be a major challenge of the future. This literature review examines theoretical frameworks that enhance Kuwaiti teachers’ knowledge and skill to adopt culturally relevant reform practices across a number of disciplines and provide guidance in an exploration and use of newer pedagogical tools like graphic organisers. It analyses the effects of graphic organisers on higher order learning and evaluates how they can effect professional development and pedagogical change in Kuwait.

The African Institute for Mathematical Sciences

Its mission is to promote Mathematics and Science in Africa and to provide a focal point for Mathematics university training in Africa. It offers scholarships for up to 50 students to come and study for a period of nine months. Of the 50 students, about 15 positions are reserved for females. In the 2006/2007 intake there were over 250 applicants. The students are housed and fed and their return travel from their home town is fully funded. Lecturers also stay at AIMS and share their meals with the students, so that a rapport quickly develops. The students are away from their families and friends for nine months and are absolutely committed to the discipline of Mathematics. When they first arrive, some of them have little ability in English but since all tuition is in English they quickly learn. Some find the transitions difficult but they all support one another and at the end of their time their English skills are very good. The students do a series of subjects that last for about three weeks each, consisting of 30 contact hours, as well as a thesis/project. Each course has a number of assignments associated with it and these get evaluated. AIMS has seven or eight teaching assistants who help with the tutorials, marking, advice, and who are a vital component of AIMS.

Spatial sciences/ surveying student BEB801 project Capstone Mini-Conference 2011

Project as a Capstone Learning Unit: Courses of the QUT Faculty of BEE seek to enable students to practice as professionals in their respective disciplines. A major part of such practice is the instigation, management,monitoring, and reporting on an urban development project. This unit offers the student a capstone learning experience near the end of their fourth year of undergraduate study. Expose the student to a set of integrated activities, each building upon the preceding, and culminating in a 'completed' project. Students apply skills and knowledge attained earlier in the course and develop new abilities for application to a real-world problem, industry or research based, to simulate the design, development and management of a project solution. These 10-12minute seminar presentations comprise the mini-conference event that are of benefit to the wider surveying and spatial science industry.