ArrayMining: a modular web-application for microarray analysis combining ensemble and consensus methods with cross-study normalization

Background: Statistical analysis of DNA microarray data provides a valuable diagnostic tool for the investigation of genetic components of diseases. To take advantage of the multitude of available data sets and analysis methods, it is desirable to combine both different algorithms and data from different studies. Applying ensemble learning, consensus clustering and cross-study normalization methods for this purpose in an almost fully automated process and linking different analysis modules together under a single interface would simplify many microarray analysis tasks. Results: We present ArrayMining.net, a web-application for microarray analysis that provides easy access to a wide choice of feature selection, clustering, prediction, gene set analysis and cross-study normalization methods. In contrast to other microarray-related web-tools, multiple algorithms and data sets for an analysis task can be combined using ensemble feature selection, ensemble prediction, consensus clustering and cross-platform data integration. By interlinking different analysis tools in a modular fashion, new exploratory routes become available, e.g. ensemble sample classification using features obtained from a gene set analysis and data from multiple studies. The analysis is further simplified by automatic parameter selection mechanisms and linkage to web tools and databases for functional annotation and literature mining. Conclusion: ArrayMining.net is a free web-application for microarray analysis combining a broad choice of algorithms based on ensemble and consensus methods, using automatic parameter selection and integration with annotation databases.

Database-backed library web sites: a case study of the use of PHP and MySQL at the University of Nottingham

This paper discusses the advantages of database-backed websites and describes the model for a library website implemented at the University of Nottingham using open source software, PHP and MySQL. As websites continue to grow in size and complexity it becomes increasingly important to introduce automation to help manage them. It is suggested that a database-backed website offers many advantages over one built from static HTML pages. These include a consistency of style and content, the ability to present different views of the same data, devolved editing and enhanced security. The University of Nottingham Library Services website is described and issues surrounding its design, technological implementation and management are explored.

Ethnicity, Social Capital and the Internet

This article explores web sites developed to express the interests and experiences of young Chinese people in Britain. Drawing on content analysis of site discussions and dialogues with site users, we argue these new communicative practices are best understood through a reworking of the social capital problematic. Firstly by recognising the irreducibility of Internet-mediated connections to the calculative instrumentalism underlying many applications of social capital theory. Secondly, by providing a more differentiated account of social capital. The interactions we explore comprise a specifically “second generation” form of social capital, cutting across the binary of bonding and bridging social capital. Thirdly judgement on the social capital consequences of Internet interactions must await a longer-term assessment of whether British Chinese institutions emerge to engage with the wider polity.

The hybrid library: a view from the UK

This paper aims to provide an overview of digital library devcelopment in the UK, concentrating on the eLib (Electronic Libraries) programme. It also discusses the idea of the Hybrid Library and considers how it fits into current electronic library developments. The paper is divided into the following areas. First, it summarises the background to the eLib programme and discusses some of its preliminary findings. It then discusses the concept of the Hybrid Library, followed by a summary of the of the current eLib (phase 3) projects which include hybrid library development projects. Finally, it identifies a number of common themes between the different projects which are currently being investigated.

La ventriloquia y el otro in El hablador de Vargas Llosa

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From "Rational Utopia" to "Will-to-Utopia". On the "Post-modern" Turn in the Recent Work of Agnes Heller

Agnes Heller recently described her position as 'postmodernist', suggesting a move from a political radical to a politically liberal or 'neoconservative' position. The aim of this paper is to assess the degree to which Heller can still be regarded as a radical political thinker through an evaluation of her work on autonomy, democracy and contingency all of which remain key concepts in her thinking about the political. We find in each case that whilst many of the motifs of her critical Marxist period recur in her recent work, they are losing their oppositional or 'negative' character in the sense that making these motifs operational would require changes to the structure or functioning of liberal-capitalism. Whils remaining in some sense a radical thinker Heller has moved from the advocacy of a 'rational utopia' to a form of theorising which I describe as 'will-to-utopia': radical at the surface yet conservative at the core.

The hybrid library: a view from the UK

This paper aims to provide an overview of digital library development in the UK, concentrating on the eLib (Electronic Libraries) programme. It also discusses the idea of the Hybrid Library and considers how it fits into current electronic library developments. The paper is divided into the following areas. First, it summarises the background to the eLib programme and discusses some of its preliminary findings. It then discusses the concept of the Hybrid Library, followed by a summary of the of the current eLib (phase 3) projects which include hybrid library development projects. Finally, it identifies a number of common themes between the different projects which are currently being investigated.

Motivation in action: A process model of L2 motivation

As part of a long-term project aimed at designing classroom interventions to motivate language learners, we have searched for a motivation model that could serve as a theoretical basis for the methodological applications. We have found that none of the existing models we considered were entirely adequate for our purpose for three reasons: (1) they did not provide a sufficiently comprehensive and detailed summary of all the relevant motivational influences on classroom behaviour; (2) they tended to focus on how and why people choose certain courses of action, while ignoring or playing down the importance of motivational sources of executing goal-directed behaviour; and (3) they did not do justice to the fact that motivation is not static but dynamically evolving and changing in time, making it necessary for motivation constructs to contain a featured temporal axis. Consequently, partly inspired by Heckhausen and Kuhl's 'Action Control Theory', we have developed a new 'Process Model of L2 Motivation', which is intended both to account for the dynamics of motivational change in time and to synthesise many of the most important motivational conceptualisations to date. In this paper we describe the main components of this model, also listing a number of its limitations which need to be resolved in future research.

Moral Requirements are still not Rational Requirements

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On the reduction theory of binary forms

Cremona developed a reduction theory for binary forms of degree 3 and 4 with integer coefficients, the motivation in the case of quartics being to improve 2-descent algorithms for elliptic curves over Q. In this paper we extend some of these results to forms of higher degree. One application of this is to the study of hyperelliptic curves.

Is Experts' Knowledge Modular?

This paper explores, both with empirical data and with computer simulations, the extent to which modularity characterises experts' knowledge. We discuss a replication of Chase and Simon's (1973) classic method of identifying 'chunks', i.e., perceptual patterns stored in memory and used as units. This method uses data about the placement of pairs of items in a memory task and consists of comparing latencies between these items and the number and type of relations they share. We then compare the human data with simulations carried out with CHREST, a computer model of perception and memory. We show that the model, based upon the acquisition of a large number of chunks, accounts for the human data well. This is taken as evidence that human knowledge is organised in a modular fashion.

Creating institutional e-print repositories

This article aims to address three questions: What are �institutional e-print repositories�? Why create them? How can they be created?