Visualising Errors in Animal Pedigree Genotype Data

Genetic analysis of a breeding animal population involves determining the inheritance pattern of genotypes for multiple genetic markers across the individuals in the population pedigree structure. However, experimental pedigree genotype data invariably contains errors in both the pedigree structure and in the associated individual genotypes, introducing inconsistencies into the dataset, rendering them useless for further analysis. The resolution of these errors requires consideration of genotype inheritance patterns in the context of the pedigree structure. Existing pedigree visualisations are typically more suited to human pedigrees and are less suitable for large complex animal pedigrees which may exhibit cross generational inbreeding. Similarly, table‐based viewers of genotype marker data can highlight where errors become apparent but lack the functionality and interactive visual feedback to allow users to locate the origin of errors within the pedigree. In this paper, we detail a design study steered by biologists who work with pedigree data, and describe successive iterations through approaches and prototypes for viewing genotyping errors in the context of a displayed pedigree. We describe how each approach performs with real pedigree genotype data and why eventually we deemed them unsuitable. Finally, a novel prototype visualisation for pedigrees, which we term the ‘sandwich view’, is detailed and we demonstrate how the approach effectively communicates errors in the pedigree context, supporting the biologist in the error identification task.     

The experience of enchantment in human–computer interaction

Improving user experience is becoming something of a rallying call in human–computer interaction but experience is not a unitary thing. There are varieties of experiences, good and bad, and we need to characterise these varieties if we are to improve user experience. In this paper we argue that enchantment is a useful concept to facilitate closer relationships between people and technology. But enchantment is a complex concept in need of some clarification. So we explore how enchantment has been used in the discussions of technology and examine experiences of film and cell phones to see how enchantment with technology is possible. Based on these cases, we identify the sensibilities that help designers design for enchantment, including the specific sensuousness of a thing, senses of play, paradox and openness, and the potential for transformation. We use these to analyse digital jewellery in order to suggest how it can be made more enchanting. We conclude by relating enchantment to varieties of experience.An earlier version of this paper was presented at Chi’2004 Fringe.     

Tracer studies on an aerated lagoon

The city of Palmerston North, New Zealand, has two aerated lagoons as its secondary treatment facility. Interest about treatment efficiency led to an investigation into the hydraulics in the second lagoon to determine if further optimisation was viable. A tracer study using rhodamine WT was undertaken to ascertain the stimulus response output. Samples were also taken at 24 points within the lagoon to determine the tracer concentration profile throughout the lagoon. The mean residence time was determined to be 39.9 h compared with a theoretical residence time of 55.4 h. Peak concentration of the tracer at the outlet occurred at 0.44 of the mean residence time. The results of the tracer study pointed to 28% of volume being dead space. A subsequent sludge survey indicated that 26% of the design volume of the lagoon was filled with sludge. While the curved geometry of the lagoon did not appear to impact the hydraulics the fact that the first aerator is confined in a relatively smaller area will have locally boosted the mixing energy input in this inlet zone. From interpretation of the tracer response and the tracer distribution profiles it appears that the aerators are mixing the influent into the bulk flow effectively in the front end of the lagoon and that there was no evidence of any substantive short-circuiting path of concentrated tracer around to the outlet. The tracer distribution profiles gave direct insight as to how the tracer was being transported within the pond and should be used more often when conducting tracer studies. Comparison with the literature indicated that the lagoon's hydraulic efficiency was on par with a baffled pond system and it would be expected that addition of several baffles to the lagoon would provide minimal further improvement.     

Clustering of high throughput gene expression data

High throughput biological data need to be processed, analyzed, and interpreted to address problems in life sciences. Bioinformatics, computational biology, and systems biology deal with biological problems using computational methods. Clustering is one of the methods used to gain insight into biological processes, particularly at the genomics level. Clearly, clustering can be used in many areas of biological data analysis. However, this paper presents a review of the current clustering algorithms designed especially for analyzing gene expression data. It is also intended to introduce one of the main problems in bioinformatics – clustering gene expression data – to the operations research community.     

Hybridization of stochastic reduced basis methods with polynomial chaos expansions

We propose a hybrid formulation combining stochastic reduced basis methods with polynomial chaos expansions for solving linear random algebraic equations arising from discretization of stochastic partial differential equations. Our objective is to generalize stochastic reduced basis projection schemes to non-Gaussian uncertainty models and simplify the implementation of higher-order approximations. We employ basis vectors spanning the preconditioned stochastic Krylov subspace to represent the solution process. In the present formulation, the polynomial chaos decomposition technique is used to represent the stochastic basis vectors in terms of multidimensional Hermite polynomials. The Galerkin projection scheme is then employed to compute the undetermined coefficients in the reduced basis approximation. We present numerical studies on a linear structural problem where the Youngs modulus is represented using Gaussian as well as lognormal models to illustrate the performance of the hybrid stochastic reduced basis projection scheme. Comparison studies with the spectral stochastic finite element method suggest that the proposed hybrid formulation gives results of comparable accuracy at a lower computational cost.     

Carbon dioxide—new uses for an old refrigerant

Carbon dioxide has been used as a refrigerant in vapour compression systems of many types for over 130 years, but it is only in the last decade that inventive minds and modern techniques have found new ways to exploit the uniquely beneficial properties of this remarkable substance. This paper traces the development of the old carbon dioxide systems, considers the technical, commercial and social reasons for their slow development and subsequent decline and examines the recent renaissance across a surprisingly broad range of applications, from trans-critical car air conditioners to low temperature industrial freezer plants. The paper then concentrates on industrial refrigeration systems, which were the basis of early developments in the period 1865–1885, but which have been somewhat overlooked in the current renaissance. The paper concludes with a review of possible future developments, indicating the areas of research and product development required to maximise the potential of the only non-toxic, non-flammable, non-ozone-depleting, non-global-warming refrigerant available for Rankine cycle vapour compression systems in the 21st century.     

Requirements for a COTS software component: A case study

The goal of the GUARDS project is to design and develop a generic fault-tolerant computer architecture that can be built from predefined standardised components. The architecture favours the use of commercial off-the-shelf (COTS) hardware and software components. However, the assessment and selection of COTS components is a non-trivial task as it requires balancing a myriad of requirements from end-users and the preliminary architecture design. In this paper, we present the requirements and assessment criteria for a specific COTS software component, the operating system kernel. As an interface specification constitutes a major compatibility criterion for the selection of COTS components in GUARDS, a particular emphasis is placed on operating system conformance to the POSIX 1003.1 standard. We discuss the general lessons learned from the assessment process and raise a number of questions relevant to the assessment of any COTS software component.     

Performance Comparison of Four Fiber-Reinforced Polymer Deck Panels

In an effort to assess the constructability and performance of bridges with fiber-reinforced polymer (FRP) composite decks, the short-term and long-term responses of a 207 m, five-span bridge retrofitted with four different FRP panel systems were monitored. The overall aspects of the panel systems, connection details, and construction techniques are presented prior to presentation of the observed and measured responses. Key design parameters (impact factors, girder distribution factors, and level of composite action) for FRP and reinforced concrete decks are evaluated. This paper demonstrates that FRP replacement decks are a viable alternative to reinforced concrete decks and identifies the differences in performances of various FRP deck systems. Two of the FRP panel systems were found to perform considerably better than the other deck systems. Issues that may reduce the service life of FRP deck systems are presented and discussed.