Open Repositories 2012

THE Open Repositories conference (OR) took place in Edinburgh in July, and showcased five days of the best the repository world has to offer. This year’s conference attracted 460 delegates from more than 40 countries, and once again showed the passion and enthusiasm of the repository community

Generative Compression

Traditional image and video compression algorithms rely on hand-crafted encoder/decoder pairs (codecs) that lack adaptability and are agnostic to the data being compressed. Here we describe the concept of generative compression, the compression of data using generative models, and suggest that it is a direction worth pursuing to produce more accurate and visually pleasing reconstructions at much deeper compression levels for both image and video data. We also demonstrate that generative compression is orders-of-magnitude more resilient to bit error rates (e.g. from noisy wireless channels) than traditional variable-length coding schemes

Non-discursive knowledge and the construction of identity. Potters, potting and performance at the bronze age tell of Százhalombatta, Hungary

This article explores the relationship between the making of things and the making of people at the Bronze Age tell at Százhalombatta, Hungary. Focusing on potters and potting, we explore how the performance of non-discursive knowledge was critical to the construction of social categories. Potters literally came into being as potters through repeated bodily enactment of potting skills. Potters also gained their identity in the social sphere through the connection between their potting performance and their audience. We trace degrees of skill in the ceramic record to reveal the material articulation of non-discursive knowledge and consider the ramifications of the differential acquisition of non-discursive knowledge for the expression of different kinds of potter's identities. The creation of potters as a social category was essential to the ongoing creation of specific forms of material culture. We examine the implications of altered potters' performances and the role of non-discursive knowledge in the construction of social models of the Bronze Ag

TREEOME: A framework for epigenetic and transcriptomic data integration to explore regulatory interactions controlling transcription

Motivation: Predictive modelling of gene expression is a powerful framework for the in silico exploration of transcriptional regulatory interactions through the integration of high-throughput -omics data. A major limitation of previous approaches is their inability to handle conditional and synergistic interactions that emerge when collectively analysing genes subject to different regulatory mechanisms. This limitation reduces overall predictive power and thus the reliability of downstream biological inference. Results: We introduce an analytical modelling framework (TREEOME: tree of models of expression) that integrates epigenetic and transcriptomic data by separating genes into putative regulatory classes. Current predictive modelling approaches have found both DNA methylation and histone modification epigenetic data to provide little or no improvement in accuracy of prediction of transcript abundance despite, for example, distinct anti-correlation between mRNA levels and promoter-localised DNA methylation. To improve on this, in TREEOME we evaluate four possible methods of formulating gene-level DNA methylation metrics, which provide a foundation for identifying gene-level methylation events and subsequent differential analysis, whereas most previous techniques operate at the level of individual CpG dinucleotides. We demonstrate TREEOME by integrating gene-level DNA methylation (bisulfite-seq) and histone modification (ChIP-seq) data to accurately predict genome-wide mRNA transcript abundance (RNA-seq) for H1-hESC and GM12878 cell lines. Availability: TREEOME is implemented using open-source software and made available as a pre-configured bootable reference environment. All scripts and data presented in this study are available online at http://sourceforge.net/projects/budden2015treeome/.Comment: 14 pages, 6 figure

Report on the 'Unlocking Attitudes to Open Access' survey, May-July 2011

As part of a nationwide project to discover more about attitudes to open access the Warwick Research Archive Portal (WRAP) team hosted a survey to allow all members of the Warwick research community, both academics and postgraduate researchers, to contribute their viewpoints to a wider survey. The wider survey is being collated by the The Repositories Support Project (RSP) as part if their work for JISC in collaboration with the United Kingdom Council of Research Repositories (UKCoRR) and it is hoped will create a nationwide picture about the opinions of UK academics on issues such as open access, intellectual property and research archives. This report presents the findings of the 71 responses received by the WRAP team and includes a series of recommendations for future advocacy and developments of both WRAP and the University of Warwick Publications service

Faraday rotation: effect of magnetic field reversals

The standard formula for the rotation measure, RM, which determines the position angle, $\psi={\rm RM}\lambda^2$, due to Faraday rotation, includes contributions only from the portions of the ray path where the natural modes of the plasma are circularly polarized. In small regions of the ray path where the projection of the magnetic field on the ray path reverses sign (called QT regions) the modes are nearly linearly polarized. The neglect of QT regions in estimating RM is not well justified at frequencies below a transition frequency where mode coupling changes from strong to weak. By integrating the polarization transfer equation across a QT region in the latter limit, I estimate the additional contribution $\Delta\psi$ needed to correct this omission. In contrast with a result proposed by \cite{BB10}, $\Delta\psi$ is small and probably unobservable. I identify a new source of circular polarization, due to mode coupling in an asymmetric QT region. I also identify a new circular-polarization-dependent correction to the dispersion measure at low frequencies.Comment: 25 pages 1 figure, accepted for publication in The Astrophysical Journa

Developing the repository manager community

This paper describes activities which have taken place within the UK institutional repository (IR) sector focusing on developing a community of practice through the sharing of experiences and best practice. This includes work done by the UK Council of Research Repositories (UKCoRR) and other bodies, together with informal activities, such as sharing the experience of organising Open Access Week events. The paper also considers future work to be undertaken by UKCoRR to continue developing the community