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.

Listening to nature : techniques for large-scale monitoring of ecosystems using acoustics

Climate change and human activity are subjecting the environment to unprecedented rates of change. Monitoring these changes is an immense task that demands new levels of automated monitoring and analysis. We propose the use of acoustics as a proxy for the time consuming auditing of fauna, especially for determining the presence/absence of species. Acoustic monitoring is deceptively simple; seemingly all that is required is a sound recorder. However there are many major challenges if acoustics are to be used for large scale monitoring of ecosystems. Key issues are scalability and automation. This paper discusses our approach to this important research problem. Our work is being undertaken in collaboration with ecologists interested both in identifying particular species and in general ecosystem health.

Listening to nature : acoustic monitoring of the environment

The requirement to monitor the rapid pace of environmental change due to global warming and to human development is producing large volumes of data but placing much stress on the capacity of ecologists to store, analyse and visualise that data. To date, much of the data has been provided by low level sensors monitoring soil moisture, dissolved nutrients, light intensity, gas composition and the like. However, a significant part of an ecologist’s work is to obtain information about species diversity, distributions and relationships. This task typically requires the physical presence of an ecologist in the field, listening and watching for species of interest. It is an extremely difficult task to automate because of the higher order difficulties in bandwidth, data management and intelligent analysis if one wishes to emulate the highly trained eyes and ears of an ecologist. This paper is concerned with just one part of the bigger challenge of environmental monitoring – the acquisition and analysis of acoustic recordings of the environment. Our intention is to provide helpful tools to ecologists – tools that apply information technologies and computational technologies to all aspects of the acoustic environment. The on-line system which we are building in conjunction with ecologists offers an integrated approach to recording, data management and analysis. The ecologists we work with have different requirements and therefore we have adopted the toolbox approach, that is, we offer a number of different web services that can be concatenated according to need. In particular, one group of ecologists is concerned with identifying the presence or absence of species and their distributions in time and space. Another group, motivated by legislative requirements for measuring habitat condition, are interested in summary indices of environmental health. In both case, the key issues are scalability and automation.

Citizen Consultation from Above and Below : The Australian Perspective

In Australia, a range of Federal Government services have been provided online for some time, but direct, online citizen consultation and involvement in processes of governance is relatively new. Moves towards more extensive citizen involvement in legislative processes are now being driven in a “top-down” fashion by government agencies, or in a “bottom-up” manner by individuals and third-sector organisations. This chapter focusses on one example from each of these categories, as well as discussing the presence of individual politicians in online social networking spaces. It argues that only a combination of these approaches can achieve effective consultation between citizens and policymakers. Existing at a remove from government sites and the frameworks for public communication which govern them, bottom-up consultation tools may provide a better chance for functioning, self-organising user communities to emerge, but they are also more easily ignored by governments not directly involved in their running. Top-down consultation tools, on the other hand, may seem to provide a more direct line of communication to relevant government officials, but for that reason are also more likely to be swamped by users who wish simply to register their dissent rather than engage in discussion. The challenge for governments, politicians, and user communities alike is to develop spaces in which productive and undisrupted exchanges between citizens and policymakers can take place.

Effects of fare collection policy on operating characteristics of a Brisbane busway station

Transit agencies across the world are increasingly shifting their fare collection mechanisms towards fully automated systems like the smart card. One of the objectives in implementing such a system is to reduce the boarding time per passenger and hence reduce the overall dwell time for the buses at the bus stops/bus rapid transit (BRT) stations. TransLink, the transit authority responsible for public transport management in South East Queensland, has introduced ‘GoCard’ technology using the Cubic platform for fare collection on its public transport system. In addition to this, three inner city BRT stations on South East Busway spine are operating as pre-paid platforms during evening peak time. This paper evaluates the effects of these multiple policy measures on operation of study busway station. The comparison between pre and post policy scenarios suggests that though boarding time per passenger has decreased, while the alighting time per passenger has increased slightly. However, there is a substantial reduction in operating efficiency was observed at the station.

Innovative cartography standards for Web-GIS portals : case study of the 'Survey of Israel's' Web-GIS Portal

Maps have been published on the world wide web since its inception (Cartwright, 1999) and are still accessed and viewed by millions of users today (Peterson, 2003). While early webbased GIS products lacked a complete set of cartographic capabilities, the functionality within such systems has significantly increased over recent years. Functionalities once found only in desktop GIS products are now available in web-based GIS applications, for example, data entry, basic editing, and analysis. Applications based on web-GIS are becoming more widespread and the web-based GIS environment is replacing the traditional desktop GIS platforms in many organizations. Therefore, development of a new cartographic method for web-based GIS is vital. The broad aim of this project is to examine and discuss the challenges and opportunities of innovative cartography methods for web-based GIS platforms. The work introduces a recently developed cartographic methodology, which is based on a web-based GIS portal by the Survey of Israel (SOI). The work discusses the prospects and constraints of such methods in improving web-GIS interfaces and usability for the end user. The work also tables the preliminary findings of the initial implementation of the web-based GIS cartographic method within the portal of the Survey of Israel, as well as the applicability of those methods elsewhere.

The measurement of applied forces during anterior single rod correction of adolescent idiopathic scoliosis

Adolescent idiopathic scoliosis (AIS) is the most common form of spinal deformity in paediatrics, prevalent in approximately 2-4% of the general population. While it is a complex three-dimensional deformity, it is clinically characterised by an abnormal lateral curvature of the spine. The treatment for severe deformity is surgical correction with the use of structural implants. Anterior single rod correction employs a solid rod connected to the anterior spine via vertebral body screws. Correction is achieved by applying compression between adjacent vertebral body screws, before locking each screw onto the rod. Biomechanical complication rates have been reported as high as 20.8%, and include rod breakage, screw pull-out and loss of correction. Currently, the corrective forces applied to the spine are unknown. These forces are important variables to consider in understanding the biomechanics of scoliosis correction. The purpose of this study was to measure these forces intra-operatively during anterior single rod AIS correction.

Youth Festival Music Performance : Kingston

Research Background - Young people with negative experiences of mainstream education often display low levels of traditional academic achievement. These young people tend to display considerable cultural and social resources developed through their repeated experiences of adversity. Education research has a duty to provide these young people with opportunities to showcase, assess and translate their social and cultural resources into symbolic forms of capital. This creative work addresses the research question, how can educators maximise the social and cultural capital they help young people acquire through live music performances and studio recordings? Research Contribution - This live music performance, built on existing artistic reputations of the artists, saw the lads support one of their local heroes from Brisbane Hip Hop music scene. In doing so they showcased what their three years of concerted musical engagement can achieve within supportive flexible learning environments. The new knowledge derived from this research focuses on the academic and self confidence benefits for disengaged young people using festival performances as authentic learning activities. Research Significance - This research is significant because it aims to maximise the number of tangible outcomes related to a school-based arts project. The young participants gained technical, artistic, social and commercial status during this project. Individual performances were distributed and downloaded via creative commons licences at the Australian Creative Resource Archive. This performance also contributed to their certified qualifications and acted as pilot research data for two competitively funded ARC grants (DP0209421 & LP0883643)

Characterising creativity : a holistic methodology for the assessment of creative works

This paper reports on the early stages of a design experiment in educational assessment that challenges the dichotomous legacy evident in many assessment activities. Combining social networking technologies with the sociology of education the paper proposes that assessment activities are best understood as a negotiable field of exchange. In this design experiment students, peers and experts engage in explicit, "front-end" assessment (Wyatt-Smith, 2008) to translate holistic judgments into institutional, and potentiality economic capital without adhering to long lists of pre-set criteria. This approach invites participants to use social networking technologies to judge creative works using scatter graphs, keywords and tag clouds. In doing so assessors will refine their evaluative expertise and negotiate the characteristics of creative works from which criteria will emerge (Sadler, 2008). The real-time advantages of web-based technologies will aggregate, externalise and democratise this transparent method of assessment for most, if not all, creative works that can be represented in a digital format.

Integrating concrete and virtual materials in an elementary mathematics classroom : a case study of success with fractions

This paper describes an approach to introducing fraction concepts using generic software tools such as Microsoft Office's PowerPoint to create "virtual" materials for mathematics teaching and learning. This approach replicates existing concrete materials and integrates virtual materials with current non-computer methods of teaching primary students about fractions. The paper reports a case study of a 12-year-old student, Frank, who had an extremely limited understanding of fractions. Frank also lacked motivation for learning mathematics in general and interacted with his peers in a negative way during mathematics lessons. In just one classroom session involving the seamless integration of off-computer and on-computer activities, Frank acquired a basic understanding of simple common equivalent fractions. Further, he was observed as the session progressed to be an enthusiastic learner who offered to share his learning with his peers. The study's "virtual replication" approach for fractions involves the manipulation of concrete materials (folding paper regions) alongside the manipulation of their virtual equivalent (shading screen regions). As researchers have pointed out, the emergence of new technologies does not mean old technologies become redundant. Learning technologies have not replaced print and oral language or basic mathematical understanding. Instead, they are modifying, reshaping, and blending the ways in which humankind speaks, reads, writes, and works mathematically. Constructivist theories of learning and teaching argue that mathematics understanding is developed from concrete to pictorial to abstract and that, ultimately, mathematics learning and teaching is about refinement and expression of ideas and concepts. Therefore, by seamlessly integrating the use of concrete materials and virtual materials generated by computer software applications, an opportunity arises to enhance the teaching and learning value of both materials.

Gender differences in children's classroom behaviour and teacher-child relationships in early childhood: An Australian Study

Background: In the early school years, children need positive attitudes to school and experiences that promote academic and social competence. Positive relationships between children and teachers make a significant contribution to school achievement and social competence. Girls are more likely to display positive classroom behaviours and positive approaches to learning than boys. Gender differences have also been noted in teacher-child relationships. This study investigated the relationship between gender differences in classroom behaviour and gender differences in teacher-child relationships in the early years. Method: Data were drawn from The Longitudinal Study of Australian Children (LSAC). LSAC is a cross-sequential cohort study funded by the Australian Government. In these analyses, Wave 1 (2004) and Wave 2 (2006) data for 4464 children in the Kindergarten Cohort were used. Children, at Wave 2, were in the early years of formal school. They had a mean age of 6.8 years (SD= 0.24). Measures included a 6-item measure of Approaches to Learning (task persistence, independence) and teacher ratings on the SDQ. Teachers rated their relationships with children on the short form of the STRS. Results: Girls were found to have more positive relationships with their teachers and to display more positive classroom behaviours than boys. Teachers described their relationships with boys as less close than their relationships with girls and rated girls as displaying more positive approaches to learning and fewer problem behaviours than boys. Positive teacher – child relationships were significantly related to more positive classroom behaviours. The quality of the teacher-child relationship at time 1 (Wave 1) was the best predictor of the quality of the teacher-child relationship at time 2 (Wave 2). Conclusions: Findings highlight the importance of developing positive learning related classroom behaviours in understanding successful school transition and the key role played by early positive teacher-child relationships in promoting school adjustment.

How do retailers from emerging markets internationalize? : The case of Chilean retailers

This paper explores how retail firms from emerging markets internationalize and compete with multinational retailers from developed markets. Drawing on interviews with company managers, industry data and corporate reports, this paper provides insights into the successful internationalization process of two Chilean retailers in the Latin American region.

Decolonising the concept of knowledge

Controlling the definition of what was essentially a subjugated culture, the colonisers reserve the power to distinguish authentic aspects of the living traditions of the colonised. If the colonised argue political demands by reference to their culture, the colonisers are quick to adjudicate what is genuine in such claims. (Fannon, 1967) Since colonial invasions, Australia’s Indigenous people have weathered rapid change. While the origins of Australia’s Indigenous peoples continues to be an archaeological interest for many, how Indigenous cultures have survived, transformed and retained a sense of ‘difference’ is fundamental to understanding the diversity of Aboriginal and Torres Strait Islander cultures within this continent as both contemporaneous and historical. It is important that teachers, students and researchers within Indigenous studies remind themselves that much of the literature on Aboriginal and Torres Strait Islanders can be ideologically traced back to the emergence of ‘knowledge’ about native peoples in the context of European imperialism and expansion from the fifteenth century. Care must therefore be taken in not conveying ‘scientific’ rational knowledge as perhaps the hidden agenda or notion of assumptions of European ‘superiority’ and non-European inferiority. The recognition by the High Court of Australia (1992) abandoned the legal myth of terra nullius which based the dispossession of Indigenous land on the basis of it being considered an empty land. It could also be argued that this decision recognised that distinct customs and traditions continue to exist within the social and cultural ‘knowledge’ of Indigenous peoples of Australia. General issues and concerns relating to research design, methodology and articulation within QUT are not just confined to this university and the research project presented as a case study but are important in dealing with how Aboriginal and Torres Strait Islander students and academics participate or are employed within the university. We feel that the design and methodology of research that either covertly or overtly focuses on Indigenous Australians can no longer presume that all research will naturally follow protocols that are culturally appropriate as this appropriateness is usually defined by the institution. By no means do we feel that research should be debilitated as a result of raising these issues, but that collaborative approaches within the ‘process’ of research will address Aboriginal and Torres Strait Islander people and communities as much as the intended outcomes of research itself.

Validation of 3D models of the outer and inner surfaces of an ovine femur

The validation of Computed Tomography (CT) based 3D models takes an integral part in studies involving 3D models of bones. This is of particular importance when such models are used for Finite Element studies. The validation of 3D models typically involves the generation of a reference model representing the bones outer surface. Several different devices have been utilised for digitising a bone’s outer surface such as mechanical 3D digitising arms, mechanical 3D contact scanners, electro-magnetic tracking devices and 3D laser scanners. However, none of these devices is capable of digitising a bone’s internal surfaces, such as the medullary canal of a long bone. Therefore, this study investigated the use of a 3D contact scanner, in conjunction with a microCT scanner, for generating a reference standard for validating the internal and external surfaces of a CT based 3D model of an ovine femur. One fresh ovine limb was scanned using a clinical CT scanner (Phillips, Brilliance 64) with a pixel size of 0.4 mm2 and slice spacing of 0.5 mm. Then the limb was dissected to obtain the soft tissue free bone while care was taken to protect the bone’s surface. A desktop mechanical 3D contact scanner (Roland DG Corporation, MDX 20, Japan) was used to digitise the surface of the denuded bone. The scanner was used with the resolution of 0.3 × 0.3 × 0.025 mm. The digitised surfaces were reconstructed into a 3D model using reverse engineering techniques in Rapidform (Inus Technology, Korea). After digitisation, the distal and proximal parts of the bone were removed such that the shaft could be scanned with a microCT (µCT40, Scanco Medical, Switzerland) scanner. The shaft, with the bone marrow removed, was immersed in water and scanned with a voxel size of 0.03 mm3. The bone contours were extracted from the image data utilising the Canny edge filter in Matlab (The Mathswork).. The extracted bone contours were reconstructed into 3D models using Amira 5.1 (Visage Imaging, Germany). The 3D models of the bone’s outer surface reconstructed from CT and microCT data were compared against the 3D model generated using the contact scanner. The 3D model of the inner canal reconstructed from the microCT data was compared against the 3D models reconstructed from the clinical CT scanner data. The disparity between the surface geometries of two models was calculated in Rapidform and recorded as average distance with standard deviation. The comparison of the 3D model of the whole bone generated from the clinical CT data with the reference model generated a mean error of 0.19±0.16 mm while the shaft was more accurate(0.08±0.06 mm) than the proximal (0.26±0.18 mm) and distal (0.22±0.16 mm) parts. The comparison between the outer 3D model generated from the microCT data and the contact scanner model generated a mean error of 0.10±0.03 mm indicating that the microCT generated models are sufficiently accurate for validation of 3D models generated from other methods. The comparison of the inner models generated from microCT data with that of clinical CT data generated an error of 0.09±0.07 mm Utilising a mechanical contact scanner in conjunction with a microCT scanner enabled to validate the outer surface of a CT based 3D model of an ovine femur as well as the surface of the model’s medullary canal.