Seed-based biclustering of gene expression data

Background Accumulated biological research outcomes show that biological functions do not depend on individual genes, but on complex gene networks. Microarray data are widely used to cluster genes according to their expression levels across experimental conditions. However, functionally related genes generally do not show coherent expression across all conditions since any given cellular process is active only under a subset of conditions. Biclustering finds gene clusters that have similar expression levels across a subset of conditions. This paper proposes a seed-based algorithm that identifies coherent genes in an exhaustive, but efficient manner. Methods In order to find the biclusters in a gene expression dataset, we exhaustively select combinations of genes and conditions as seeds to create candidate bicluster tables. The tables have two columns: (a) a gene set, and (b) the conditions on which the gene set have dissimilar expression levels to the seed. First, the genes with less than the maximum number of dissimilar conditions are identified and a table of these genes is created. Second, the rows that have the same dissimilar conditions are grouped together. Third, the table is sorted in ascending order based on the number of dissimilar conditions. Finally, beginning with the first row of the table, a test is run repeatedly to determine whether the cardinality of the gene set in the row is greater than the minimum threshold number of genes in a bicluster. If so, a bicluster is outputted and the corresponding row is removed from the table. Repeating this process, all biclusters in the table are systematically identified until the table becomes empty. Conclusions This paper presents a novel biclustering algorithm for the identification of additive biclusters. Since it involves exhaustively testing combinations of genes and conditions, the additive biclusters can be found more readily.

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

Detaining the usual suspects : charting the use of segregated settings in New South Wales government schools, Australia

In this paper, we examine the increase in segregated placements in the New South Wales government school sector. Using disaggregated enrolment data, we point to the growing over-representation of boys in special schools and classes; particularly those of a certain age in certain support categories. In the discussion that follows, we question the role of special education in the development of new and additional forms of being “at risk.” In effect, we invert the traditional concept by asking: Who is at risk of what? In focusing on the containment of risk, are modern practices of diagnosis and segregation perpetuating risks that already disproportionately affect certain groups of individuals? Do these perceptions of and responses to risk in local schools now place these students at greater personal risk of school failure and a future marked by social exclusion? And, finally, is that risk worth the cost?

Using mobile technology and augmented reality to increase data reliability for environmental assessment

Climate change and land use pressures are making environmental monitoring increasingly important. As environmental health is degrading at an alarming rate, ecologists have tried to tackle the problem by monitoring the composition and condition of environment. However, traditional monitoring methods using experts are manual and expensive; to address this issue government organisations designed a simpler and faster surrogate-based assessment technique for consultants, landholders and ordinary citizens. However, it remains complex, subjective and error prone. This makes collected data difficult to interpret and compare. In this paper we describe a work-in-progress mobile application designed to address these shortcomings through the use of augmented reality and multimedia smartphone technology.

Surviving an avalanche of data

Open the sports or business section of your daily newspaper, and you are immediately bombarded with an array of graphs, tables, diagrams, and statistical reports that require interpretation. Across all walks of life, the need to understand statistics is fundamental. Given that our youngsters’ future world will be increasingly data laden, scaffolding their statistical understanding and reasoning is imperative, from the early grades on. The National Council of Teachers of Mathematics (NCTM) continues to emphasize the importance of early statistical learning; data analysis and probability was the Council’s professional development “Focus of the Year” for 2007–2008. We need such a focus, especially given the results of the statistics items from the 2003 NAEP. As Shaughnessy (2007) noted, students’ performance was weak on more complex items involving interpretation or application of items of information in graphs and tables. Furthermore, little or no gains were made between the 2000 NAEP and the 2003 NAEP studies. One approach I have taken to promote young children’s statistical reasoning is through data modeling. Having implemented in grades 3 –9 a number of model-eliciting activities involving working with data (e.g., English 2010), I observed how competently children could create their own mathematical ideas and representations—before being instructed how to do so. I thus wished to introduce data-modeling activities to younger children, confi dent that they would likewise generate their own mathematics. I recently implemented data-modeling activities in a cohort of three first-grade classrooms of six year- olds. I report on some of the children’s responses and discuss the components of data modeling the children engaged in.

OpenRatSLAM : an open source brain-based SLAM system

RatSLAM is a navigation system based on the neural processes underlying navigation in the rodent brain, capable of operating with low resolution monocular image data. Seminal experiments using RatSLAM include mapping an entire suburb with a web camera and a long term robot delivery trial. This paper describes OpenRatSLAM, an open-source version of RatSLAM with bindings to the Robot Operating System framework to leverage advantages such as robot and sensor abstraction, networking, data playback, and visualization. OpenRatSLAM comprises connected ROS nodes to represent RatSLAM’s pose cells, experience map, and local view cells, as well as a fourth node that provides visual odometry estimates. The nodes are described with reference to the RatSLAM model and salient details of the ROS implementation such as topics, messages, parameters, class diagrams, sequence diagrams, and parameter tuning strategies. The performance of the system is demonstrated on three publicly available open-source datasets.

Design of open source framework for traffic and travel simulation

For the evaluation, design, and planning of traffic facilities and measures, traffic simulation packages are the de facto tools for consultants, policy makers, and researchers. However, the available commercial simulation packages do not always offer the desired work flow and flexibility for academic research. In many cases, researchers resort to designing and building their own dedicated models, without an intrinsic incentive (or the practical means) to make the results available in the public domain. To make matters worse, a substantial part of these efforts pertains to rebuilding basic functionality and, in many respects, reinventing the wheel. This problem not only affects the research community but adversely affects the entire traffic simulation community and frustrates the development of traffic simulation in general. For this problem to be addressed, this paper describes an open source approach, OpenTraffic, which is being developed as a collaborative effort between the Queensland University of Technology, Australia; the National Institute of Informatics, Tokyo; and the Technical University of Delft, the Netherlands. The OpenTraffic simulation framework enables academies from geographic areas and disciplines within the traffic domain to work together and contribute to a specific topic of interest, ranging from travel choice behavior to car following, and from response to intelligent transportation systems to activity planning. The modular approach enables users of the software to focus on their area of interest, whereas other functional modules can be regarded as black boxes. Specific attention is paid to a standardization of data inputs and outputs for traffic simulations. Such standardization will allow the sharing of data with many existing commercial simulation packages.

Collaborating to develop research data management services and collections

The Queensland University of Technology (QUT) Library, like many other academic and research institution libraries in Australia, has been collaborating with a range of academic and service provider partners to develop a range of research data management services and collections. Three main strategies are being employed and an overview of process, infrastructure, usage and benefits is provided of each of these service aspects. The development of processes and infrastructure to facilitate the strategic identification and management of QUT developed datasets has been a major focus. A number of Australian National Data Service (ANDS) sponsored projects - including Seeding the Commons; Metadata Hub / Store; Data Capture and Gold Standard Record Exemplars have / will provide QUT with a data registry system, linkages to storage, processes for identifying and describing datasets, and a degree of academic awareness. QUT supports open access and has established a culture for making its research outputs available via the QUT ePrints institutional repository. Incorporating open access research datasets into the library collections is an equally important aspect of facilitating the adoption of data-centric eresearch methods. Some datasets are available commercially, and the library has collaborated with QUT researchers, in the QUT Business School especially strongly, to identify and procure a rapidly growing range of financial datasets to support research. The library undertakes licensing and uses the Library Resource Allocation to pay for the subscriptions. It is a new area of collection development for with much to be learned. The final strategy discussed is the library acting as “data broker”. QUT Library has been working with researchers to identify these datasets and undertake the licensing, payment and access as a centrally supported service on behalf of researchers.

Strategies for gaining and maintaining academic support for the institutional open access repository

The impact of research can be measured by use or citation count. The more widely available that research outputs are; the more likely they are to be used, and the higher the impact. Making the author-manuscript version of research outputs freely available via the institutional repository greatly increases the availability of research outputs and can increase the impact. QUT ePrints, the open access institutional repository of research outputs at Queensland University of Technology (QUT), Australia, was established in 2003 and is managed by the QUT Library. The repository now contains over 39,000 records. More than 21,000 of these records have full-text copies attached as result of continuous effort to maintain momentum and encourage academic engagement. The full-text deposit rate has continued to increase over time and, in 2012 (August, at the time of writing), 88% of the records for works published in 2012 provide access to a full-text copy. Achieving success has required a long term approach to collaboration, open access advocacy, repository promotion, support for the deposit process, and ongoing system development. This paper discusses the various approaches adopted by QUT Library, in collaboration with other areas of the University, to achieve success. Approaches include mainstreaming the repository via having it report to the University Research and Innovation Committee; regular provision of deposit rate data to faculties; championing key academic supporters; and holding promotional competitions and events such as during Open Access Week. Support and training is provided via regular deposit workshops with academics and faculty research support groups and via the provision of online self-help information. Recent system developments have included the integration of citation data (from Scopus and Web of Science) and the development of a statistical reporting system which incentivise engagement.

Groundwater visualisation system (GVS) : a software framework for integrated display and interrogation of conceptual hydrogeological models, data and time-series animation

Management of groundwater systems requires realistic conceptual hydrogeological models as a framework for numerical simulation modelling, but also for system understanding and communicating this to stakeholders and the broader community. To help overcome these challenges we developed GVS (Groundwater Visualisation System), a stand-alone desktop software package that uses interactive 3D visualisation and animation techniques. The goal was a user-friendly groundwater management tool that could support a range of existing real-world and pre-processed data, both surface and subsurface, including geology and various types of temporal hydrological information. GVS allows these data to be integrated into a single conceptual hydrogeological model. In addition, 3D geological models produced externally using other software packages, can readily be imported into GVS models, as can outputs of simulations (e.g. piezometric surfaces) produced by software such as MODFLOW or FEFLOW. Boreholes can be integrated, showing any down-hole data and properties, including screen information, intersected geology, water level data and water chemistry. Animation is used to display spatial and temporal changes, with time-series data such as rainfall, standing water levels and electrical conductivity, displaying dynamic processes. Time and space variations can be presented using a range of contouring and colour mapping techniques, in addition to interactive plots of time-series parameters. Other types of data, for example, demographics and cultural information, can also be readily incorporated. The GVS software can execute on a standard Windows or Linux-based PC with a minimum of 2 GB RAM, and the model output is easy and inexpensive to distribute, by download or via USB/DVD/CD. Example models are described here for three groundwater systems in Queensland, northeastern Australia: two unconfined alluvial groundwater systems with intensive irrigation, the Lockyer Valley and the upper Condamine Valley, and the Surat Basin, a large sedimentary basin of confined artesian aquifers. This latter example required more detail in the hydrostratigraphy, correlation of formations with drillholes and visualisation of simulation piezometric surfaces. Both alluvial system GVS models were developed during drought conditions to support government strategies to implement groundwater management. The Surat Basin model was industry sponsored research, for coal seam gas groundwater management and community information and consultation. The “virtual” groundwater systems in these 3D GVS models can be interactively interrogated by standard functions, plus production of 2D cross-sections, data selection from the 3D scene, rear end database and plot displays. A unique feature is that GVS allows investigation of time-series data across different display modes, both 2D and 3D. GVS has been used successfully as a tool to enhance community/stakeholder understanding and knowledge of groundwater systems and is of value for training and educational purposes. Projects completed confirm that GVS provides a powerful support to management and decision making, and as a tool for interpretation of groundwater system hydrological processes. A highly effective visualisation output is the production of short videos (e.g. 2–5 min) based on sequences of camera ‘fly-throughs’ and screen images. Further work involves developing support for multi-screen displays and touch-screen technologies, distributed rendering, gestural interaction systems. To highlight the visualisation and animation capability of the GVS software, links to related multimedia hosted online sites are included in the references.

One-stop government portals : transformation or navigation?

E-government is seen as a promising approach for governments to improve their service towards citizens and become more cost-efficient in service delivery. This is often combined with one-stop government, which is a citizen-oriented approach stressing integrated provision of services from multiple departments via a single access point, the one-stop government portal. While the portal concept is gaining prominence in practice, there is little know about its status in academic literature. This hinders academics in building an accumulated body of knowledge around the concept and makes it hard for practitioners to access relevant academic insights on the topic. The objective of this study is to identify and understand the key themes of the one-stop government portal concept in academic, e-government research. A holistic analysis is provided by addressing different viewpoints: social-political, legal, organizational, user, security, service, data & information, and technical. As overall finding we conclude that there are two different approaches: a more pragmatic approach focuses on quick wins in particular related to usability and navigation and a more ambitious, transformational approach having far reaching social-political, legal, organizational implications.

Reconnection : a contemporary development in cultural landscape theory contributing to rehabilitation strategies for Australian open-cut coal mining landscapes

A value-shift began to influence global political thinking in the late 20th century, characterised by recognition of the need for environmentally, socially and culturally sustainable resource development. This shift entailed a move away from thinking of ‘nature’ and ‘culture’ as separate entities – the former existing to serve the latter – toward the possibility of embracing the intrinsic worth of the nonhuman world. Cultural landscape theory recognises ‘nature’ as at once both ‘natural’, and a ‘cultural’ construct. As such, it may offer a framework through which to progress in the quest for ‘sustainable development’. This study makes a contribution to this quest by asking whether contemporary developments in cultural landscape theory can contribute to rehabilitation strategies for Australian open-cut coal mining landscapes. The answer is ‘yes’. To answer the research question, a flexible, ‘emergent’ methodological approach has been used, resulting in the following outcomes. A thematic historical overview of landscape values and resource development in Australia post-1788, and a review of cultural landscape theory literature, contribute to the formation of a new theoretical framework: Reconnecting the Interrupted Landscape. This framework establishes a positive answer to the research question. It also suggests a method of application within the Australian open-cut coal mining landscape, a highly visible exemplar of the resource development landscape. This method is speculatively tested against the rehabilitation strategy of an operating open-cut coal mine, concluding with positive recommendations to the industry, and to government.

New and young firms Entrepreneurship policy and the role of government – evidence from the Federation of Small Businesses survey

Purpose – The purpose of this paper is to investigate whether new and young firms are different from older firms. This analysis is undertaken to explore general characteristics, use of external resources and growth orientation. Design/methodology/approach – Data from the 2008 UK Federation of Small Businesses survey provided 8,000 responses. Quantitative analysis identified significantly different characteristics of firms from 0-4, 4-9, 9-19 and 20+ years. Factor analysis was utilised to identify the advice sets, finance and public procurement customers of greatest interest, with ANOVA used to statistically compare firms in the identified age groups with different growth aspirations. Findings – The findings reveal key differences between new, young and older firms in terms of characteristics including business sector, owner/manager age, education/business experience, legal status, intellectual property and trading performance. New and young firms were more able to access beneficial resources in terms of finance and advice from several sources. New and young firms were also able to more easily access government and external finance, as well as government advice, but less able to access public procurement. Research limitations/implications – New and young firms are utilising external networks to access several resources for development purposes, and this differs for older firms. This suggests that a more explicit age-differentiated focus is required for government policies aimed at supporting firm growth. Originality/value – The study provides important baseline data for future quantitative and qualitative studies focused on the impact of firm age and government policy.

Perceptions and expectations for learning and development for older workers within Queensland local government councils : a case study

Current literature warns organisations about a global ageing phenomenon. Workplace ageing is causing a diminishing work pool which has consequences for a sustainable workforce in the future. This phenomenon continues to impact on local government councils in Australia. Australia has one of the world’s most rapidly ageing populations, and there is evidence that Australian local government councils are already resulting in an unsustainable workforce. Consequently, this research program investigated the role of older workers in the Queensland local government workplace in enabling them to extend their working lives towards transitional employment and a sustainable workforce in the future. Transitional Employment is intended as a strategy for enabling individuals to have greater control over their employment options and their employability during the period leading to their final exit from the workforce. There was no evidence of corporate support for older workers in Queensland local government councils other than tokenistic government campaigns encouraging organisations to "better value their older workers". (Queensland Government, 2007d, p.6). TE is investigated as a possible intervention for older workers in the future. The international and national literature review reflected a range of matters impacting on current older workers in the workforce and barriers preventing them from accessing services towards extending their employment beyond the traditional retirement age (60 years) as defined by the Australian Government; an age when individuals can access their superannuation. Learning and development services were identified as one of those barriers. There was little evidence of investment in or consistent approaches to supporting older workers by organisations. Learning and development services appeared at best to be ad hoc, reactive to corporate productivity and outputs with little recognition of the ageing phenomenon (OECD, 2006, p.23) and looming skills and labour shortages (ALGA, 2006, p. 19). Themes from the literature review led to the establishment of three key research questions: 1. What are the current local government workforce issues impacting on skills and labour retention? 2. What are perceptions about the current workplace environment? And, 3. What are the expectations about learning and development towards extending employability of older workers within the local government sector? The research questions were explored by utilising three qualitative empirical studies, using some numerical data for reporting and comparative analysis. Empirical Study One investigated common themes for accessing transitional employment and comprised two phases. A literature review and Study One data analysis enabled the construction of an initial Transitional Employment Model which includes most frequent themes. Empirical Study Two comprised focus groups to further consider those themes. This led to identification of issues impacting the most on access to learning and development by older workers and towards a revised TEM. Findings presented majority support for transitional employment as a strategy for supporting older workers to work beyond their traditional retirement age. Those findings are presented as significant issues impacting on access to transitional employment within the final 3-dimensionsal TEM. The model is intended as a guide for responding to an ageing workforce by local government councils in the future. This study argued for increased and improved corporate support, particularly for learning and development services for older workers. Such support will enable older workers to maintain their employability and extend their working lives; a sustainable workforce in the future.

Future Information Communication Technology and Applications : ICFICE 2013

Focuses on the various aspects of advances in future information communication technology and its applications Presents the latest issues and progress in the area of future information communication technology Applicable to both researchers and professionals These proceedings are based on the 2013 International Conference on Future Information & Communication Engineering (ICFICE 2013), which will be held at Shenyang in China from June 24-26, 2013. The conference is open to all over the world, and participation from Asia-Pacific region is particularly encouraged. The focus of this conference is on all technical aspects of electronics, information, and communications ICFICE-13 will provide an opportunity for academic and industry professionals to discuss the latest issues and progress in the area of FICE. In addition, the conference will publish high quality papers which are closely related to the various theories and practical applications in FICE. Furthermore, we expect that the conference and its publications will be a trigger for further related research and technology improvements in this important subject. "This work was supported by the NIPA (National IT Industry Promotion Agency) of Korea Grant funded by the Korean Government (Ministry of Science, ICT & Future Planning)."