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.

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.

Effect of family relatedness on characteristics of estimated IBD probabilities in relation to precision of QTL estimates

Background: A random QTL effects model uses a function of probabilities that two alleles in the same or in different animals at a particular genomic position are identical by descent (IBD). Estimates of such IBD probabilities and therefore, modeling and estimating QTL variances, depend on marker polymorphism, strength of linkage and linkage disequilibrium of markers and QTL, and the relatedness of animals in the pedigree. The effect of relatedness of animals in a pedigree on IBD probabilities and their characteristics was examined in a simulation study. Results: The study based on nine multi-generational family structures, similar to a pedigree structure of a real dairy population, distinguished by an increased level of inbreeding from zero to 28 % across the studied population. Highest inbreeding level in the pedigree, connected with highest relatedness, was accompanied by highest IBD probabilities of two alleles at the same locus, and by lower relative variation coefficients. Profiles of correlation coefficients of IBD probabilities along the marked chromosomal segment with those at the true QTL position were steepest when the inbreeding coefficient in the pedigree was highest. Precision of estimated QTL location increased with increasing inbreeding and pedigree relatedness. A method to assess the optimum level of inbreeding for QTL detection is proposed, depending on population parameters. Conclusions: An increased overall relationship in a QTL mapping design has positive effects on precision of QTL position estimates. But the relationship of inbreeding level and the capacity for QTL detection depending on the recombination rate of QTL and adjacent informative marker is not linear. © 2010 Freyer et al., licensee BioMed Central Ltd.

Open Access Books

Although digital technology has, in theory, made it possible for many more people to access content at no extra cost, fewer people than ever before are able to read the books written by university-based researchers. This article looks, very briefly, at the role that open access licenses might play in reviving the scholarly monograph: a specialised area of academic publishing that has seen sales decline by more than 90% over the past three decades. It also introduces a new approach to funding open-access scholarly books being pioneered by the not-for-profit social enterprise Knowledge Unlatched.

Open source information retrieval : a report on the SIGIR 2012 workshop

On August 16, 2012 the SIGIR 2012 Workshop on Open Source Information Retrieval was held as part of the SIGIR 2012 conference in Portland, Oregon, USA. There were 2 invited talks, one from industry and one from academia. There were 6 full papers and 6 short papers presented as well as demonstrations of 4 open source tools. Finally there was a lively discussion on future directions for the open source Information Retrieval community. This contribution discusses the events of the workshop and outlines future directions for the community.

Mapping quantitative trait loci in a wild population using linkage and linkage disequilibrium analyses

Historical information can be used, in addition to pedigree, traits and genotypes, to map quantitative trait locus (QTL) in general populations via maximum likelihood estimation of variance components. This analysis is known as linkage disequilibrium (LD) and linkage mapping, because it exploits both linkage in families and LD at the population level. The search for QTL in the wild population of Soay sheep on St. Kilda is a proof of principle. We analysed the data from a previous study and confirmed some of the QTLs reported. The most striking result was the confirmation of a QTL affecting birth weight that had been reported using association tests but not when using linkage-based analyses. Copyright © Cambridge University Press 2010.

Prediction of IBD based on population history for fine gene mapping

A novel multiple regression method (RM) is developed to predict identity-by-descent probabilities at a locus L (IBDL), among individuals without pedigree, given information on surrounding markers and population history. These IBDL probabilities are a function of the increase in linkage disequilibrium (LD) generated by drift in a homogeneous population over generations. Three parameters are sufficient to describe population history: effective population size (Ne), number of generations since foundation (T), and marker allele frequencies among founders (p). IBD L are used in a simulation study to map a quantitative trait locus (QTL) via variance component estimation. RM is compared to a coalescent method (CM) in terms of power and robustness of QTL detection. Differences between RM and CM are small but significant. For example, RM is more powerful than CM in dioecious populations, but not in monoecious populations. Moreover, RM is more robust than CM when marker phases are unknown or when there is complete LD among founders or Ne is wrong, and less robust when p is wrong. CM utilises all marker haplotype information, whereas RM utilises information contained in each individual marker and all possible marker pairs but not in higher order interactions. RM consists of a family of models encompassing four different population structures, and two ways of using marker information, which contrasts with the single model that must cater for all possible evolutionary scenarios in CM.

Mapping of multiple quantitative trait loci affecting bovine spongiform encephalopathy

A whole-genome scan was conducted to map quantitative trait loci (QTL) for BSE resistance or susceptibility. Cows from four half-sib families were included and 173 microsatellite markers were used to construct a 2835-cM (Kosambi) linkage map covering 29 autosomes and the pseudoautosomal region of the sex chromosome. Interval mapping by linear regression was applied and extended to a multiple-QTL analysis approach that used identified QTL on other chromosomes as cofactors to increase mapping power. In the multiple-QTL analysis, two genome-wide significant QTL (BTA17 and X/Y ps) and four genome-wide suggestive QTL (BTA1, 6, 13, and 19) were revealed. The QTL identified here using linkage analysis do not overlap with regions previously identified using TDT analysis. One factor that may explain the disparity between the results is that a more extensive data set was used in the present study. Furthermore, methodological differences between TDT and linkage analyses may affect the power of these approaches.

From movie screens to moving screens : mapping qualities of new urban interactions

Next generation screens of diverse dimensions such as the Pebble e-paper watch, Google’s Project Glass, Microsoft’s Kinect and IllumiRoom, and large-scale multi-touch screen surface areas, increasingly saturate and diversify the urban mediascape. This paper seeks to contribute to media architecture and interaction design theory by starting to critically examine how these different screen formats are creating a ubiquitous screen mediascape across the city. We introduce next generation personal, domestic, and public screens. The paper critically challenges conventional dichotomies such as local / global, online / offline, private / public, large / small, mobile / static, that have been created in the past to describe some of the qualities and characteristics of interfaces and their usage. More and more scholars recognise that the black and white nature of these dichotomies does not adequately represent the fluid and agile capabilities of many new screen interfaces. With this paper, we hope to illustrate the more nuanced ‘trans-scalar’ qualities of these new urban interactions, that is, ways in which they provide a range functionality, without being locked into either end of a scale.

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.

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.

Knowledge unlatched : towards an open and networked future for academic publishing

Specialist book length publications in the humanities and social sciences (including but not exclusively monographs) are experiencing a crisis. It is clear that the current publishing system is failing both the producers and users of scholarship and neglects many of the opportunities associated with networked culture.

3D thermal mapping of building interiors using an RGB-D and thermal camera

The building sector is the dominant consumer of energy and therefore a major contributor to anthropomorphic climate change. The rapid generation of photorealistic, 3D environment models with incorporated surface temperature data has the potential to improve thermographic monitoring of building energy efficiency. In pursuit of this goal, we propose a system which combines a range sensor with a thermal-infrared camera. Our proposed system can generate dense 3D models of environments with both appearance and temperature information, and is the first such system to be developed using a low-cost RGB-D camera. The proposed pipeline processes depth maps successively, forming an ongoing pose estimate of the depth camera and optimizing a voxel occupancy map. Voxels are assigned 4 channels representing estimates of their true RGB and thermal-infrared intensity values. Poses corresponding to each RGB and thermal-infrared image are estimated through a combination of timestamp-based interpolation and a pre-determined knowledge of the extrinsic calibration of the system. Raycasting is then used to color the voxels to represent both visual appearance using RGB, and an estimate of the surface temperature. The output of the system is a dense 3D model which can simultaneously represent both RGB and thermal-infrared data using one of two alternative representation schemes. Experimental results demonstrate that the system is capable of accurately mapping difficult environments, even in complete darkness.

Open Simulator BPMN Process Model Editor

Video presented as part of APCCM 2010 conference in Brisbane Australia. Video illustrating the main components of an Open Simulator BPMN Editor we have developed.