REAPR: a universal tool for genome assembly evaluation.

Methods to reliably assess the accuracy of genome sequence data are lacking. Currently completeness is only described qualitatively and mis-assemblies are overlooked. Here we present REAPR, a tool that precisely identifies errors in genome assemblies without the need for a reference sequence. We have validated REAPR on complete genomes or de novo assemblies from bacteria, malaria and Caenorhabditis elegans, and demonstrate that 86% and 82% of the human and mouse reference genomes are error-free, respectively. When applied to an ongoing genome project, REAPR provides corrected assembly statistics allowing the quantitative comparison of multiple assemblies. REAPR is available at http://www.sanger.ac.uk/resources/software/reapr/

Non-Euclidean principal component analysis by Hebbian learning

Principal component analysis based on Hebbian learning is originally designed for data processing inEuclidean spaces. We present in this contribution an extension of Oja's Hebbian learning approach fornon-Euclidean spaces. We show that for Banach spaces the Hebbian learning can be carried out using theunderlying semi-inner product. Prominent examples for such Banach spaces are the lp-spaces for p≠2.For kernels spaces, as applied in support vector machines or kernelized vector quantization, thisapproach can be formulated as an online learning scheme based on the differentiable kernel. Hence,principal component analysis can be explicitly carried out in the respective data spaces but nowequipped with a non-Euclidean metric. In the article we provide the theoretical framework and giveillustrative examples

Summary of Research Conducted by the Manufacturing Systems Team 1994-2002

The Manufacturing Systems team was one of the research teams within the Lean Aerospace Initiative (LAI) whose goal was to document, analyze and communicate the design attributes and relationships that lead to significant performance improvements in manufacturing systems in the defense aerospace industry. This report will provide an integrated record of this research using the Production Operations Transition to Lean Roadmap as its organizing framework

Free Podcasts: Didaktische Produktion von Open Educational Resources

Podcasts werden immer häufiger auch im Hochschulbereich eingesetzt. Oft handelt es sich dabei um Aufzeichnungen von Lehrveranstaltungen. Dieser Beitrag stellt ein Vorgehensmodell in den Vordergrund, das hilft, Podcasts zu produzieren, die frei zugänglich, zugleich aber auch didaktisch hochwertig sind und somit im wahrsten Sinne als „Open Educational Resources“ bezeichnet werden können. Das Vorgehensmodell erfasst sechs zentrale Themenbereiche (Zielgruppe, didaktisches Ziel, Autor/in, Inhalt, technisches Format und Gestaltung), die es bei der Konzipierung von Podcasts als OER zu beachten gilt. Damit leistet das Vorgehensmodell auch einen Beitrag zur Qualitätssicherung von Podcast-Produktionen. (DIPF/ Orig.

Place, memory, and identity in the Vietnamese diaspora

This thesis traces the twin themes of place and memory in the lives of a displaced people who experience life in Australia through the life left behind. This study begins with the notion that identity is spatially encoded , and that the modes of defining the self are physically and metaphorically grounded in space. The ongoing relationship with Vietnam connects people through time and space with a mythologised place that lies within the landscape of memory but has existential immediacy. I examine the degrees of separation from the symbolic landscape of Vietnam that are invoked in the reconstruction of identity that occurs after migration. The significance of the spatial dimension of migration has been explored in several different domains. I begin by providing a background to the displacement process through a historical account of the transformations in Vietnamese national identity, and the events that led to mass migration out of the country. Through the personal accounts of these processes by Vietnamese people, I detail the response to the arrival of Vietnamese people by Australian society, and the changes within the Vietnamese communities over the last twenty years. I then examine the construction of Vietnamese spaces within Australia beginning with the embodied differences of Vietnamese-Australians, leading out through domestic spaces, and streetscapes to the use of public spaces. I reveal the way in which both fragmentation and consolidation of family ties are experienced spatially. I explore the spaces in which the body moves as well as the spaces of Vietnamese homes to draw out the explicit and implicit meanings encoded in domestic landscapes and the material arrangements of social space. Relationships between different Vietnamese familes and communities are also examined in spatial terms as is the relationship of Vietnamese communities to the broader Australian society. The relationship that Vietnamese people have with Vietnam is examined through people's memories as well as through their ongoing relations with their homeland and with family and friends elsewhere in the diaspora. By studying the changes in the relationship that Vietnamese people have with their homeland I explore the geopolitical landscape that invests the lives of Vietnamese-Australians with the past, in another time and space. Borderlands are formed within the broader Australian community as well as in relation to an imaginary past and present homeland. The creativity of diasporas in constantly changing circumstances is tempered by the will to create immutable borders on both sides of a cultural divide. The chimera of boundaries is revealed through the highlighting of diversity and transformation in individual people's lives, in relationships within and beyond families, and in the Australian urban environment. By tracing the power and potency of 'home' and the memories of other times and places in the lives of Vietnamese migrants in Australia, some of the threads in the complex weaving of identity in the lives of Vietnamese Australians are revealed. The capturing of the past in the present is explored, particularly in relation to places that have been lived in in the past, and spaces in urban Australia which Vietnamese people now inhabit. Constructions of the past are unravelled through a study of memories, fantasies, narratives and myths. The hidden dimensions of marginality are examined through a study of the spatial politics of difference within urban Australia, within the overarching historical and political contexts of Vietnamese migration. The identities of Vietnamese people have been infused with new meanings as people's lives undergo transformation within the changing environmental and cultural worlds of Australia where they are impacted upon by the expectations and responses of mainstream society. The spatial configurations of Vietnamese-Australian identities are explored in order to understand the possibilities for both freedom and subjection offered by a new country and to evaluate the multiple meanings of home

Summary of Research Conducted by the Manufacturing Systems Team

The Manufacturing Systems team is one of the focus groups within the Lean Aerospace Initiative whose goal is to document, analyze and communicate the design attributes and relationships that lead to significant performance improvements in manufacturing systems in the defense aerospace industry. This paper will provide a usable record of what work has been done by the Manufacturing Systems team and it is aimed at releasing research conducted by the LAI in the field of manufacturing systems. The purpose of this paper is to present the research conducted by the Manufacturing Systems team in the framework provided by the Transition-To-Lean Roadmap. The research results are presented briefly within this framework and each phase of the paper ends with and extensive list of resources for further reference

A Machine Learning-Based Raman Spectroscopic Assay for the Identification of Burkholderia mallei and Related Species

Burkholderia (B.) mallei, the causative agent of glanders, and B. pseudomallei, the causative agent of melioidosis in humans and animals, are genetically closely related. The high infectious potential of both organisms, their serological cross-reactivity, and similar clinical symptoms in human and animals make the differentiation from each other and other Burkholderia species challenging. The increased resistance against many antibiotics implies the need for fast and robust identification methods. The use of Raman microspectroscopy in microbial diagnostic has the potential for rapid and reliable identification. Single bacterial cells are directly probed and a broad range of phenotypic information is recorded, which is subsequently analyzed by machine learning methods. Burkholderia were handled under biosafety level 1 (BSL 1) conditions after heat inactivation. The clusters of the spectral phenotypes and the diagnostic relevance of the Burkholderia spp. were considered for an advanced hierarchical machine learning approach. The strain panel for training involved 12 B. mallei, 13 B. pseudomallei and 11 other Burkholderia spp. type strains. The combination of top- and sub-level classifier identified the mallei-complex with high sensitivities (>95%). The reliable identification of unknown B. mallei and B. pseudomallei strains highlighted the robustness of the machine learning-based Raman spectroscopic assay