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.

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.

How well are Australian children doing in the first year of school : a demographic analysis

Background: The transition to school is a sensitive period for children in relation to school success. In the early school years, children need to develop positive attitudes to school and have experiences that promote academic, behavioural and social competence. When children begin school there are higher expectations of responsibility and independence and in the year one class, there are more explicit academic goals for literacy and numeracy and more formal instruction. Most importantly, children’s early attitudes to learning and learning styles have an impact on later educational outcomes. 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 2 (2006) data for 2499 children in the Kindergarten Cohort were used. Children, at Wave 2, were in the first year of formal school. They had a mean age of 6.9 years (SD= 0.26). Measures included a 6-item measure of Approaches to Learning (task persistence, independence) and the Academic Rating Scales for language and literacy and mathematical thinking. Teachers rated their relationships with children on the short form of the STRS. Results: Girls were rated by their teachers as doing better than boys on Language and literacy, Approaches to learning; and they had a better relationship with their teacher. Children from an Aboriginal or Torres Strait Island (ATSI) background were rated as doing less well on Language and Literacy and Mathematical thinking and on their Approaches to learning. Children from high Socio Economic Position families are doing better on teacher rated Language and Literacy, Mathematical thinking, Approaches to learning and they had a better relationship with their teacher. Conclusions: Findings highlight the importance of key demographic variables in understanding children’s early school success.

How the whiteness embedded in health services impacts on the health and well-being of Aboriginal peoples

Aboriginal women are treated differently by non-indigenous health care providers based on perceptions of Aboriginality and skin colour and white race privilege within health care environments. The experiences shared below are from some of the Aboriginal woman respondents in a research project undertaken within Rockhampton, a regional area in Central Queensland (Fredericks, 2003). The experiences give an insight into how the Aboriginal women interviewed felt and their observations of how other Aboriginal women were treated within health care settings based on skin colour and perceptions of Aboriginality. A number of the women demonstrated a personal in-depth analysis of the issues surrounding place, skin colour and Aboriginality. For example, one of the women, who I named Kay, identified one particular health service organisation and stated that, ‘it is a totally white designed space. There is nothing that identifies me to that place. I just won’t go there as a client because I don’t feel they cater for me as a black woman’. Kay’s words give us an understanding of the reality experienced by Aboriginal women as they move in and out of places within health environments and broader society. Some of these experiences are examples of direct racism, whilst other examples are subtle and demonstrate how whiteness manifests and plays out within places. I offer acknowledgement and honour to the Aboriginal women who shared their stories and gave me a glimpse of their realities in the research project from which the findings presented in this chapter are taken. It is to this research project that is the subject of this chapter.

Incorporating an economic model in the health impact assessment approach

The current policy decision making in Australia regarding non-health public investments (for example, transport/housing/social welfare programmes) does not quantify health benefits and costs systematically. To address this knowledge gap, this study proposes an economic model for quantifying health impacts of public policies in terms of dollar value. The intention is to enable policy-makers in conducting economic evaluation of health effects of non-health policies and in implementing policies those reduce health inequalities as well as enhance positive health gains of the target population. Health Impact Assessment (HIA) provides an appropriate framework for this study since HIA assesses the beneficial and adverse effects of a programme/policy on public health and on health inequalities through the distribution of those effects. However, HIA usually tries to influence the decision making process using its scientific findings, mostly epidemiological and toxicological evidence. In reality, this evidence can not establish causal links between policy and health impacts since it can not explain how an individual or a community reacts to changing circumstances. The proposed economic model addresses this health-policy linkage using a consumer choice approach that can explain changes in group and individual behaviour in a given economic set up. The economic model suggested in this paper links epidemiological findings with economic analysis to estimate the health costs and benefits of public investment policies. That is, estimating dollar impacts when health status of the exposed population group changes by public programmes – for example, transport initiatives to reduce congestion by building new roads/ highways/ tunnels etc. or by imposing congestion taxes. For policy evaluation purposes, the model is incorporated in the HIA framework by establishing association among identified factors, which drive changes in the behaviour of target population group and in turn, in the health outcomes. The economic variables identified to estimate the health inequality and health costs are levels of income, unemployment, education, age groups, disadvantaged population groups, mortality/morbidity etc. However, though the model validation using case studies and/or available database from Australian non-health policy (say, transport) arena is in the future tasks agenda, it is beyond the scope of this current paper.

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.

A reflective model for colour studies learning

In a university context how should colour be taught in order to engage students? Entwistle states, ‘What we learn depends on how we learn, and why we have to learn it.’ Therefore, there is a need to address the accumulating evidence that highlights the effects of learning environments on the quality of student learning when considering colour education. It is necessary to embrace the contextual demands while ensuring that the student knowledge of colour and the joy of discovering its characteristics in practice are enhanced. Institutional policy is forcing educators to re-evaluate traditional studio’s effectiveness and the intensive 'hands-on' interactive approach that is embedded in such an approach. As curriculum development involves not only theory and project work, the classroom culture and physical environment also need to be addressed. The increase in student numbers impacting the number of academic staff/student ratio, availability of teaching support as well as increasing variety of student age, work commitments, learning styles and attitudes have called for positive changes to how we teach. The Queensland University of Technology’s restructure in 2005 was a great opportunity to re-evaluate and redesign the approach to teaching within the design units of Interior Design undergraduate program –including colour. The resultant approach “encapsulates a mode of delivery, studio structure, as well as the learning context in which students and staff interact to facilitate learning”1 with a potential “to be integrated into a range of Interior Design units as it provides an adaptive educational framework rather than a prescriptive set of rules”.

Property Education : an evaluation of how well undergraduate property students are prepared for commencing their careers

The evolution of property education to adapt to the changing business environment requires changes to course content, method of delivery and assessment. Many universities have a special interest in understanding how the students transition in and transition out of the property programs. The impact of the first year student experience is often easier to assess through students’ progression in the course and performance in their intermediate and advanced units. However, the students’ success in transitioning from university student to property professional is often more difficult to determine. In an environment where many property students commence their professional careers while still completing their undergraduate property qualification, a survey of current final year students was undertaken to identify the students’ perception of their level of preparedness for entry into the professional world. This study has also been informed by feedback received from and informal discussions held with industry representative bodies, alumni and senior members of professional organisations. The QUT UD40 Bachelor of Urban Development, Property Economics course has been designed to achieve graduate capabilities in core technical skills and generic professional skills which are required by property professionals. The results of this study were that some units in the program were perceived to provide direct preparation for students commencing their professional careers whilst the impact of other units was less tangible. Valuable feedback received during the study included an assessment of the relevance of many multi-disciplinary units, the appropriateness of the programming of units within the course and the appropriateness of repetition of content during the course. The further research question arises as to how universities can better assist students in the transition to the professional environment when frequently this occurs prior to completion of the property course.

Humanistic science education : moves from within and challenges from without

For a number of years now it has been evident that the major issue facing science educators in the more developed countries of the world is the quantitative decline in enrolments in the senior secondary sciences, particularly the physical sciences, and in the number of higher achieving students applying for places in universities to undertake further studies in science. The deep malaise in school science to which these quantitative measures point has been elucidated by more qualitative studies of the students’ experience of studying science in secondary school in several of these countries (Sweden, Lindahl (2003); England, Simon and Osborne (2002); and Australia, Lyons (2005)). Remarkably concordant descriptions of these experiences can be summarized as: School science is: • transmission of knowledge from the teacher or the textbook to the students. • about content that is irrelevant and boring to our lives. • difficult to learn in comparison with other subjects Incidentally, the Australian study only involved consistently high achieving students; but even so, most of them found science more difficult than other more interesting subjects, and concluded that further science studies should be avoided unless they were needed for some career purpose. Other more representative confirmations of negative evaluations of the science curricula across Australia (and in particular states) are now available in Australia, from the large scale reviews of Goodrum, Hackling and Rennie (2001) and from the TIMSS (2002). The former reported that well under half of secondary students find the science at school relevant to my future, useful ion everyday life, deals with things I am concerned with and helps me make decisions about my health.. TIMSS found that 62 and 65 % of females and males in Year 4 agree with I like learning science, but by Year 8 only 26 and 33 % still agree. Students in Japan have been doubly notably because of (a) their high performance in international measures of science achievement like TIMSS and PISA and (b) their very low response to items in these studies which relate to interest in science. Ogura (2003) reported an intra-national study of students across Years 6-9 (upper primary through Junior High); interest in a range of their subjects (including science) that make up that country’s national curriculum. There was a steady decline in interest in all these subjects which might have indicated an adolescent reaction against schooling generally. However, this study went on to ask the students a further question that is very meaningful in the Japanese context, If you discount the importance of this subject for university entrance, is it worth studying? Science and mathematics remained in decline while all the other subjects were seen more positively. It is thus ironic, at a time when some innovations in curriculum and other research-based findings are suggesting ways that these failures of school science might be corrected, to find school science under a new demands that come from quite outside science education, and which certainly do not have the correction of this malaise as a priority. The positive curricular and research findings can be characterized as moves from within science education, whereas the new demands are moves that come from without science education. In this paper I set out these two rather contrary challenges to the teaching of science as it is currently practised, and go on to suggest a way forward that could fruitfully combine the two.

How well are Australian children doing in the first year of school?

Background: The transition to school is a sensitive period for children in relation to school success. In the early school years, children need to develop positive attitudes to school and have experiences that promote academic, behavioural and social competence. When children begin school there are higher expectations of responsibility and independence and in the year one class, there are more explicit academic goals for literacy and numeracy and more formal instruction. Most importantly, children’s early attitudes to learning and learning styles have an impact on later educational outcomes. 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 2 (2006) data for 2499 children in the Kindergarten Cohort were used. Children, at Wave 2, were in the first year of formal school. They had a mean age of 6.9 years (SD= 0.26). Measures included a 6-item measure of Approaches to Learning (task persistence, independence) and the Academic Rating Scales for language and literacy and mathematical thinking. Teachers rated their relationships with children on the short form of the STRS. Results: Girls were rated by their teachers as doing better than boys on Language and literacy, Approaches to learning; and they had a better relationship with their teacher. Children from an Aboriginal or Torres Strait Island (ATSI) background were rated as doing less well on Language and Literacy and Mathematical thinking and on their Approaches to learning. Children from high Socio Economic Position families are doing better on teacher rated Language and Literacy, Mathematical thinking, Approaches to learning and they had a better relationship with their teacher. Conclusions: Findings highlight the importance of key demographic variables in understanding children’s early school success.

AITPM Email Newsletter Volume 0905, May 2009: Presidents Message

President’s Message Hello fellow AITPM members, We’ve been offered a lot of press lately about the Federal Government’s plan for the multibillion dollar rollout of its high speed broadband network, which at the moment is being rated to a speed of 100Mb/s. This seems fantastic in comparison to the not atypical 250 to 500kb/s that I receive on my metropolitan cable broadband, which incidentally my service provider rates at theoretical speeds of up to 8 Mb/s. I have no doubt that such a scheme will generate significant advantages to business and consumers. However, I also have some reservations. Only a few of years ago I marvelled at my first 256Mb USB stick, which cost my employer about $90. Last month I purchased a 16Gb stick with a free computer carry bag for $80, which on the back of my envelope has given me about 72 times the value of my first USB stick not including the carry bag! I am pretty sure the technology industry will find a way to eventually push a lot more than 100Mb/s down the optic fibre network just as they have done with pushing several Mb/s ADSL2 down antique copper wire. This makes me wonder about the general problem of inbuilt obsolescence of all things high-tech due to rapid advances in the tech industry. As a transport professional I then think to myself that our industry has been moving forward at somewhat of a slower pace. We certainly have had major milestones having significant impacts, such as the move from horse and cart to the self propelled motor vehicle, sealing and formal geometric design of roads, development of motorways, signalisation of intersections, coordination of networks, to simulation modelling for real time adaptive control (perhaps major change has been at a frequency of 30 years or so?). But now with ITS truly penetrating the transport market, largely thanks to the in-car GPS navigator, smart phone, e-toll and e-ticket, I believe that to avoid our own obsolescence we’re going to need to “plan for ITS” rather than just what we seem to have been doing up until now, that is, to get it out there. And we’ll likely need to do it at a faster pace. It will involve understanding how to data mine enormous data sets, better understanding the human/machine interface, keeping pace with automotive technology more closely, resolving the ethical and privacy chestnuts, and in the main actually planning for ITS to make peoples’ lives easier rather than harder. And in amongst this we’ll need to keep pace with the types of technology advances similar to my USB stick example above. All the while we’ll be making a brand new set of friends in the disciplines that will morph into ITS along with us. Hopefully these will all be “good” problems for our profession to have. I should close in reminding everyone again that AITPM’s flagship event, the 2009 AITPM National Conference, Traffic Beyond Tomorrow, is being held in Adelaide from 5 to 7 August. www.aitpm.com has all of the details about how to register, sponsor a booth, session, etc. Best regards all, Jon Bunker

AITPM Email Newsletter Volume 0905, June 2009 : President's Message

President’s Message Hello fellow AITPM members, Due to three colliding forces of nature I find myself writing this month’s message from home – today, I am still getting over a persistent virus that seemed to set in just after returning from Singapore a couple of weeks ago, which my diabetes won’t let me get away with too easily (no Kermit the Frog swine flu jokes please). Combine this with a very wet day in Brisbane – in fact the wettest for 20 years (how can we complain, except for flash flooding?). And in Queensland today is a state school teachers’ strike, so one half of our brood is over watching TV. Family snapshots aside, the biggest news for our industry of late is the $8.5 billion announced in the Federal Budget for transport infrastructure projects; many “shovel ready”, but some – and fortunate for our profession – desktop ready. This newsletter provides nationwide coverage on the transport infrastructure aspects of the Federal Budget. We’ll need a bit more time to carefully look at the ensuing State Budgets’ announcements. Regarding the federal budget announcements, I am pleased to see serious attention being paid to upgrading the M1 system – I hope to see a motorway standard facility connecting Adelaide to at least Rockhampton in my lifetime. But some other important roads are of course missing out in this particular budget. Various levels of commitment are being made to urban passenger rail – some project significant while others planning significant. Enhancement of suburban rail is important across the capitals and Australia’s medium sized cities such as the Gold Coast and Newcastle. Not much on road safety initiatives jumped out at me, but I believe it is implied in the large road projects and in some of the detail elsewhere. I do believe it’s about time a ‘Vision Zero’ style policy is adopted at the National level, since any death is unacceptable on the road, just as it is in any other workplace. So, overall some good news on building transport infrastructure to keep the economy purring during this recession, and strongly supporting it during future boom times. The other edge to the sword, of course, is that we tax payers will be paying a considerable amount for borrowings for these projects over a long period of time. I close again in reminding everyone again that AITPM’s flagship event, the 2009 AITPM National Conference, Traffic Beyond Tomorrow, is being held in Adelaide from 5 to 7 August. www.aitpm.com has all of the details about how to register, sponsor a booth, session, etc. Best regards all, Jon Bunker

AITPM Email Newsletter Volume 0910, October 2009 : Presidents Message

President’s Message Hello fellow AITPM members, Well I can’t believe it’s already October! My office is already organising its end of year function and looking to plan for 2010. Our whole School is moving to a different building next year, with the lovely L block eventually making way for a new shiny one. Those of you who have entered the Brisbane CBD from the south side, across the Captain Cook Bridge, would know L block as the big 9 storey brick and concrete Lego block ode to 1970’s functional architecture, which greets you on the right hand side. Onto traffic matters: an issue that has been tossing around in my mind of late is that of speed. I know I am growing older and may be prematurely becoming a “grumpy old man”, but everyone around me locally seems to be accelerating off from the stop line much faster than I was taught to for economical driving, both here and in the United States (yes they made my wife and me resit our written and practical driving tests when we lived there). People here in Australia also seem to be driving right on top of the posted speed limit, on whichever part of the Road Hierarchy, whether urban or rural. I was also taught on both sides of the planet that the posted speed limit is a maximum legal speed, not the recommended driving speed. This message did seem to sink in to the American drivers around me when we lived in Oregon - where people did appear to drive more cautiously. Further, posted speed limits in Oregon were, and I presume still are, set more conservative by about 5mph or 10km/h than Australian limits, for any given part of the Road Hierarchy. Another excellent speed limit treatment used in Oregon was in school zones, where reduced speed limits applied “when children are present” rather than during prescribed hours on school days. This would be especially useful here in Australia, where a lot of extra-curricular activities take place around schools outside of the prescribed speed limit hours. Before and after hours school care is on the increase (with parents dropping and collecting children near dawn and dusk in the winter), and many childcentred land uses are located adjacent to schools, such as Scouts/Guides halls, swimming pools and parks. Consequentially, I believe there needs to be some consideration towards more public campaigning about economical driving and the real purpose of the speed limit = or perhaps even a rethink of the speed limit concept, if people really are driving on top of it and it’s not just me becoming grumpier (our industrial psychology friends at the research centres may be able to assist us here). The Queensland organising committee is now in full swing organising the 2010 AITPM National Conference, What’s New?, so please keep a lookout for related content. Best regards to all, Jon Bunker PS A Cartoonists view of traffic engineers I thought you might enjoy this. http://xkcd.com/277/

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.

Towards an acoustic environmental observatory

The need for large scale environmental monitoring to manage environmental change is well established. Ecologists have long used acoustics as a means of monitoring the environment in their field work, and so the value of an acoustic environmental observatory is evident. However, the volume of data generated by such an observatory would quickly overwhelm even the most fervent scientist using traditional methods. In this paper we present our steps towards realising a complete acoustic environmental observatory - i.e. a cohesive set of hardware sensors, management utilities, and analytical tools required for large scale environmental monitoring. Concrete examples of these elements, which are in active use by ecological scientists, are also presented