miRDeep*: an integrated application tool for miRNA identification from RNA sequencing data

miRDeep and its varieties are widely used to quantify known and novel micro RNA (miRNA) from small RNA sequencing (RNAseq). This article describes miRDeep*, our integrated miRNA identification tool, which is modeled off miRDeep, but the precision of detecting novel miRNAs is improved by introducing new strategies to identify precursor miRNAs. miRDeep* has a user-friendly graphic interface and accepts raw data in FastQ and Sequence Alignment Map (SAM) or the binary equivalent (BAM) format. Known and novel miRNA expression levels, as measured by the number of reads, are displayed in an interface, which shows each RNAseq read relative to the pre-miRNA hairpin. The secondary pre-miRNA structure and read locations for each predicted miRNA are shown and kept in a separate figure file. Moreover, the target genes of known and novel miRNAs are predicted using the TargetScan algorithm, and the targets are ranked according to the confidence score. miRDeep* is an integrated standalone application where sequence alignment, pre-miRNA secondary structure calculation and graphical display are purely Java coded. This application tool can be executed using a normal personal computer with 1.5 GB of memory. Further, we show that miRDeep* outperformed existing miRNA prediction tools using our LNCaP and other small RNAseq datasets. miRDeep* is freely available online at http://www.australianprostatecentre.org/research/software/mirdeep-star

Information practices of teen content creators : the intersection of action and experiences a grounded theory study

What are the information practices of teen content creators? In the United States over two thirds of teens have participated in creating and sharing content in online communities that are developed for the purpose of allowing users to be producers of content. This study investigates how teens participating in digital participatory communities find and use information as well as how they experience the information. From this investigation emerged a model of their information practices while creating and sharing content such as film-making, visual art work, story telling, music, programming, and web site design in digital participatory communities. The research uses grounded theory methodology in a social constructionist framework to investigate the research problem: what are the information practices of teen content creators? Data was gathered through semi-structured interviews and observation of teen’s digital communities. Analysis occurred concurrently with data collection, and the principle of constant comparison was applied in analysis. As findings were constructed from the data, additional data was collected until a substantive theory was constructed and no new information emerged from data collection. The theory that was constructed from the data describes five information practices of teen content creators. The five information practices are learning community, negotiating aesthetic, negotiating control, negotiating capacity, and representing knowledge. In describing the five information practices there are three necessary descriptive components, the community of practice, the experiences of information and the information actions. The experiences of information include information as participation, inspiration, collaboration, process, and artifact. Information actions include activities that occur in the categories of gathering, thinking and creating. The experiences of information and information actions intersect in the information practices, which are situated within the specific community of practice, such as a digital participatory community. Finally, the information practices interact and build upon one another and this is represented in a graphic model and explanation.

Changing lanes

The purpose of Changing Lanes was to question the identity of Brisbane laneways through the collaboration of local stakeholders by promoting design. Community partners provided design briefs for student work from Architecture and Interior Design to be included in a design competition. Shortlisted student projects were featured in the Changing Lanes event during which the winners were announced. In addition to student work from Architecture and Interior Design, the five other disciplines from QUT's School of Design also exhibited samples of student work. The engagement of local stakeholders; architectural practice, interior designers, engineers, and a media and publication agency was fundamental to the success of this event. The design work on display provided creative expression for the potential of Brisbane Laneways to bring communities together through the language of design. An underutilised area of Fortitude Valley was activated through a combination of media including drawings, videos, street furniture, and music.

Ian Weir Research Architect : website

Research background: Communicating the diverse nature of multimodal practice is inherently difficult for the design-led research academic. Websites are an effective means of displaying images and text, but for the user/viewer the act of viewing is often random and disorienting, due to the non-linear means of accessing the information. This characteristic of websites limits the medium’s efficacy in regard to presenting an overarching philosophical standpoint or theme - the key driver behind most academic research. Research Contribution: This website: http://www.ianweirarchitect.com, presents a means of reconciling this problem by presenting a deceptively simple graphic and temporal layout, which limits the opportunity for the user/viewer to become disoriented and miss the key themes and issues that binds, the otherwise divergent, research material together. Research significance: http://www.ianweirarchitect.com, is a creative work that supplements Dr Ian Weir’s exhibition “Enacted Cartography” held in August 2012 in Brisbane and in August/September 2012 in Venice, Italy for the 13th International Architecture Exhibition (Venice Architecture Biennale). Dr Weir was selected by the Australian Institute of Architects to represent innovation in architectural practice for the Institute’s Formations: New Practices in Australian Architecture, exhibition and catalogue (of the same name) held in the Australian Pavilion, The Giardini, Venice. This website is creative output that compliments Dr Weir’s other multimodal outputs including photographic artworks, cartographic maps and architectural designs.

Custom digital workflows : a new framework for design analysis integration

Flexible information exchange is critical to successful design-analysis integration, but current top-down, standards-based and model-oriented strategies impose restrictions that contradicts this flexibility. In this article we present a bottom-up, user-controlled and process-oriented approach to linking design and analysis applications that is more responsive to the varied needs of designers and design teams. Drawing on research into scientific workflows, we present a framework for integration that capitalises on advances in cloud computing to connect discrete tools via flexible and distributed process networks. We then discuss how a shared mapping process that is flexible and user friendly supports non-programmers in creating these custom connections. Adopting a services-oriented system architecture, we propose a web-based platform that enables data, semantics and models to be shared on the fly. We then discuss potential challenges and opportunities for its development as a flexible, visual, collaborative, scalable and open system.

Custom digital workflows : a new framework for design analysis integration

Flexible information exchange is critical to successful design integration, but current top-down, standards-based and model-oriented strategies impose restrictions that are contradictory to this flexibility. In this paper we present a bottom-up, user-controlled and process-oriented approach to linking design and analysis applications that is more responsive to the varied needs of designers and design teams. Drawing on research into scientific workflows, we present a framework for integration that capitalises on advances in cloud computing to connect discrete tools via flexible and distributed process networks. Adopting a services-oriented system architecture, we propose a web-based platform that enables data, semantics and models to be shared on the fly. We discuss potential challenges and opportunities for the development thereof as a flexible, visual, collaborative, scalable and open system.

Glider path-planning for optimal sampling of mesocale eddies

Ocean gliders constitute an important advance in the highly demanding ocean monitoring scenario. Their effciency, endurance and increasing robustness make these vehicles an ideal observing platform for many long term oceanographic applications. However, they have proved to be also useful in the opportunis-tic short term characterization of dynamic structures. Among these, mesoscale eddies are of particular interest due to the relevance they have in many oceano-graphic processes.

Wicked futures : metadesign, resilience and transformative classrooms

This paper presents an Australian case study entitled “Designing Futures”. It examines a six month multidisciplinary design program offered by a large co-educational, inner-city state school in Queensland in 2011. The program extended an already successful and innovative school-based design curriculum and involved students in Philosophy, Science, Mathematics and English classes, as well those in Art and Design. Additionally, there were 5 full-day workshops where students combined a wide range of skills to brainstorm, design and create sustainable solutions. The design thinking used in this program was based on the concepts of metadesign, design activism and design futuring. “Designing Futures” linked over 700 middle and secondary school students and staff with nine designers-in-residence from diverse disciplines, including bio-ethics. The program aimed to empower students from highly diverse cultural and social backgrounds to engage in authentic, participatory design processes, prepare them for future social and environmental challenges, and increase personal and community resilience. The research results will inform ongoing program development and research in K-12 design education, both within the school and in conjunction with university and community partnerships in Queensland.

Towards a secure human-and-computer mutual authentication protocol

We blend research from human-computer interface (HCI) design with computational based crypto- graphic provable security. We explore the notion of practice-oriented provable security (POPS), moving the focus to a higher level of abstraction (POPS+) for use in providing provable security for security ceremonies involving humans. In doing so we high- light some challenges and paradigm shifts required to achieve meaningful provable security for a protocol which includes a human. We move the focus of security ceremonies from being protocols in their context of use, to the protocols being cryptographic building blocks in a higher level protocol (the security cere- mony), which POPS can be applied to. In order to illustrate the need for our approach, we analyse both a protocol proven secure in theory, and a similar proto- col implemented by a �nancial institution, from both HCI and cryptographic perspectives.

Games for change and transformative learning : an ethnographic case study

This thesis aims to contribute to a better understanding of how serious games/games for change function as learning frameworks for transformative learning in an educational setting. This study illustrates how the meaning-making processes and learning with and through computer gameplay are highly contingent, and are significantly influenced by the uncertainties of the situational context. The study focuses on SCAPE, a simulation game that addresses urban planning and sustainability. SCAPE is based on the real-world scenario of Kelvin Grove Urban Village, an inner city redevelopment area in Brisbane, Queensland, Australia. The game is embedded within an educational program, and I thus account for the various gameplay experiences of different school classes participating in this program. The networks emerging from the interactions between students/players, educators, facilitators, the technology, the researcher, as well as the setting, result in unanticipated, controversial, and sometimes unintended gameplay experiences and outcomes. To unpack play, transformative learning and games, this study adopts an ecological approach that considers the magic circle of gameplay in its wider context. Using Actor-Network Theory as the ontological lens for inquiry, the methods for investigation include an extensive literature review, ethnographic participant observation of SCAPE, as well as student and teacher questionnaires, finishing with interviews with the designers and facilitators of SCAPE. Altogether, these methods address my research aim to better understand how the heterogeneous actors engage in the relationships in and around gameplay, and illustrate how their conflicting understandings enable, shape or constrain the (transformative) learning experience. To disentangle these complexities, my focus continuously shifts between the following modes of inquiry into the aims „h To describe and analyse the game as a designed artefact. „h To examine the gameplay experiences of players/students and account for how these experiences are constituted in the relationships of the network. „h To trace the meaning-making processes emerging from the various relations of players/students, facilitators, teachers, designers, technology, researcher, and setting, and consider how the boundaries of the respective ecology are configured and negotiated. „h To draw out the implications for the wider research area of game-based learning by using the simulation game SCAPE as an example for introducing gameplay to educational settings. Accounting in detail for five school classes, these accounts represent, each in its own right, distinct and sometimes controversial forms of engagement in gameplay. The practices and negotiations of all the assembled human and non-human actors highlight the contingent nature of gameplay and learning. In their sum, they offer distinct but by no means exhaustive examples of the various relationships that emerge from the different assemblages of human and non-human actors. This thesis, hence, illustrates that game-based learning in an educational setting is accompanied by considerable unpredictability and uncertainty. As ordinary life spills and leaks into gameplay experiences, group dynamics and the negotiations of technology, I argue that overly deterministic assertions of the game¡¦s intention, as well as a too narrowly defined understanding of the transformative learning outcome, can constrain our inquiries and hinder efforts to further elucidate and understand the evolving uncertainties around game-based learning. Instead, this thesis posits that playing and transformative learning are relational effects of the respective ecology, where all actors are networked in their (partial) enrolment in the process of translation. This study thus attempts to foreground the rich opportunities for exploring how game-based learning is assembled as a network of practices.

Libraries as co-working spaces : understanding user motivations and perceived barriers to social learning

This paper aims to inform design strategies for smart space technology to enhance libraries as environments for co-working and informal social learning. The focus is on understanding user motivations, behaviour, and activities in the library when there is no programmed agenda. The study analyses gathered data over five months of ethnographic research at ‘The Edge’ – a bookless library space at the State Library of Queensland in Brisbane, Australia, that is explicitly dedicated to co-working, social learning, peer collaboration, and creativity around digital culture and technology. The results present five personas that embody people’s main usage patterns as well as motivations, attitudes, and perceived barriers to social learning. It appears that most users work individually or within pre-organised groups, but usually do not make new connections with co-present, unacquainted users. Based on the personas, four hybrid design dimensions are suggested to improve the library as a social interface for shared learning encounters across physical and digital spaces. The findings in this paper offer actionable knowledge for managers, decision makers, and designers of technology-enhanced library spaces and similar collaboration and co-working spaces.

Adaptive teachers embracing new ways of learning with robotics in Chinese schools

In July 2010, China announced the “National Plan for Medium and Long-term Education Reform and Development(2010-2020)” (PRC 2010). The Plan calls for an education system that: • promotes an integrated development which harnesses everyone’s talent; • combines learning and thinking; unifies knowledge and practice; • allows teachers to teach according to individuals’ needs; and • reforms education quality evaluation and personnel evaluation systems focusing on performance including character, knowledge, ability and other factors. This paper discusses the design and implementation of a Professional Learning Program (PLP) undertaken by 432 primary, middle and high school teachers in China. The aim of this initiative was to develop adaptive expertise in using technology that facilitated innovative science and technology teaching and learning as envisaged by the Chinese Ministry of Education’s (2010-2020) education reforms. Key principles derived from literature about professional learning and scaffolding of learning informed the design of the PLP. The analysis of data revealed that the participants had made substantial progress towards the development of adaptive expertise. This was manifested not only by advances in the participants’ repertoires of Subject Matter Knowledge and Pedagogical Content Knowledge but also in changes to their levels of confidence and identities as teachers. It was found that through time the participants had coalesced into a professional learning community that readily engaged in the sharing, peer review, reuse and adaption, and collaborative design of innovative science and technology learning and assessment activities.

Daylighting design and simulation : ease of use analysis of digital tools for architects

Good daylighting design in buildings not only provides a comfortable luminous environment, but also delivers energy savings and comfortable and healthy environments for building occupants. Yet, there is still no consensus on how to assess what constitutes good daylighting design. Currently amongst building performance guidelines, Daylighting factors (DF) or minimum illuminance values are the standard; however, previous research has shown the shortcomings of these metrics. New computer software for daylighting analysis contains new more advanced metrics for daylighting (Climate Base Daylight Metrics-CBDM). Yet, these tools (new metrics or simulation tools) are not currently understood by architects and are not used within architectural firms in Australia. A survey of architectural firms in Brisbane showed the most relevant tools used by industry. The purpose of this paper is to assess and compare these computer simulation tools and new tools available architects and designers for daylighting. The tools are assessed in terms of their ease of use (e.g. previous knowledge required, complexity of geometry input, etc.), efficiency (e.g. speed, render capabilities, etc.) and outcomes (e.g. presentation of results, etc. The study shows tools that are most accessible for architects, are those that import a wide variety of files, or can be integrated into the current 3d modelling software or package. These software’s need to be able to calculate for point in times simulations, and annual analysis. There is a current need in these software solutions for an open source program able to read raw data (in the form of spreadsheets) and show that graphically within a 3D medium. Currently, development into plug-in based software’s are trying to solve this need through third party analysis, however some of these packages are heavily reliant and their host program. These programs however which allow dynamic daylighting simulation, which will make it easier to calculate accurate daylighting no matter which modelling platform the designer uses, while producing more tangible analysis today, without the need to process raw data.

Teaching and learning family and consumer sciences through K-W-L charts

While much of the control and many of the activities found in today’s classrooms have been placed in the hands of the learners and learning has become inquiry-based, there remains a need for teachers to use teaching tools that would facilitate this student-centered teaching process. This article identifies the K-W-L Chart as one such tool and follows a case study of four Kuwaiti ‘Family and Consumer Sciences’ teaching / learning events to evaluate their ability to enhance the learning outcomes of eight students. The research was designed from a qualitative, multi-tiered design approach and was assessed through a constant comparative method of data analysis of interview responses, classroom observations and worksheet-assessments. The results showed that the use of K-W-L Charts influenced the teachers and learners toward a more inquiry-based approach and facilitated a more student-centered and collaborative learning environment, raising the level of interest and the amount of personal input given by the students.

Schools as meeting places : critical and inclusive literacies in changing local environments

Schools bring people together. Yet for many children there are major discontinuities between their lives in and out of school and such differences impact on literacy teaching and learning in both predictable and unpredictable ways. However if schools were reconceptualised as meeting places, where different people are thrown together (Massey, 2005) curriculum and pedagogy could be designed to take into account students’ and teachers’ different experiences and histories and to make those differences a resource for literacy learning. This paper draws on a long-term project with administrators and teachers working in a school situated in a site of urban regeneration and significant demographic shifts. It draws particularly on the ways in which one teacher re-positioned her grade 4/5 students as researchers, designers and journalists exploring student and staff memories of a school. It argues that place, and people’s relationships with places, can be a rich resource for literacy learning when teachers make it the object of study.