Casting Polymer Nets to Optimize Noisy Molecular Codes

Life relies on the efficient performance of molecular codes, which relate symbols and meanings via error-prone molecular recognition. We describe how optimizing a code to withstand the impact of molecular recognition noise may be approximated by the statistics of a two-dimensional network made of polymers. The noisy code is defined by partitioning the space of symbols into regions according to their meanings. The "polymers" are the boundaries between these regions and their statistics defines the cost and the quality of the noisy code. When the parameters that control the cost-quality balance are varied, the polymer network undergoes a first-order transition, where the number of encoded meanings rises discontinuously. Effects of population dynamics on the evolution of molecular codes are discussed.Comment: PNAS 200

Reproducibility in Research: Systems, Infrastructure, Culture

The reproduction and replication of research results has become a major issue for a number of scientific disciplines. In computer science and related computational disciplines such as systems biology, the challenges closely revolve around the ability to implement (and exploit) novel algorithms and models. Taking a new approach from the literature and applying it to a new codebase frequently requires local knowledge missing from the published manuscripts and transient project websites. Alongside this issue, benchmarking, and the lack of open, transparent and fair benchmark sets present another barrier to the verification and validation of claimed results. In this paper, we outline several recommendations to address these issues, driven by specific examples from a range of scientific domains. Based on these recommendations, we propose a high-level prototype open automated platform for scientific software development which effectively abstracts specific dependencies from the individual researcher and their workstation, allowing easy sharing and reproduction of results. This new e-infrastructure for reproducible computational science offers the potential to incentivise a culture change and drive the adoption of new techniques to improve the quality and efficiency – and thus reproducibility – of scientific exploration.Royal Society UR

Performance, Politics and Media: How the 2010 British General Election leadership debates generated ‘talk’ amongst the electorate.

During the British General Election 2010 a major innovation was introduced in part to improve engagement: a series of three live televised leadership debates took place where the leader of each of the three main parties, Labour, Liberal Democrat and Conservative, answered questions posed by members of the public and subsequently debated issues pertinent to the questions. In this study we consider these potentially ground breaking debates as the kind of event that was likely to generate discussion. We investigate various aspects of the ‘talk’ that emerged as a result of watching the debates. As an exploratory study concerned with situated accounts of the participants experiences we take an interpretive perspective. In this paper we outline the meta-narratives (of talk) associated with the viewing of the leadership debates that were identified, concluding our analysis by suggesting that putting a live debate on television and promoting and positioning it as a major innovation is likely to mean that is how the audience will make sense of it – as a media event

Exploring UK crime networks

This paper describes our experiences with three different crime networks in the UK: burglary, 'gun' gangs and retail theft. We present an introduction into each of these problems, and highlight some of the issues related to over-simplification of the network analysis. We also review the term `third-generation' analysis, and provide some insights into achieving this, but also conclude that it can be an extremely computationally expensive undertaking

Measuring UK crime gangs

This paper describes the output of a study to tackle the problem of gang-related crime in the UK; we present the intelligence and routinely gathered data available to a UK regional police force, and describe an initial social network analysis of gangs in the Greater Manchester area of the UK between 2000-2006. By applying social network analysis techniques, we attempt to detect the birth of two new gangs based on local features (modularity, cliques) and global features (clustering coefficient). Thus for the future, identifying the changes in these can help us identify the possible birth of new gangs (sub-networks) in the social system. Furthermore, we study the dynamics of these networks globally and locally, and have identified the global characteristics that tell us that they are not random graphs - they are small world graphs - implying that the formation of gangs is not a random event. However, we are not yet able to conclude anything significant about scale-free characteristics due to insufficient sample size

Synchronized dynamics of cortical neurons with time-delay feedback

The dynamics of three mutually coupled cortical neurons with time delays in the coupling are explored numerically and analytically. The neurons are coupled in a line, with the middle neuron sending a somewhat stronger projection to the outer neurons than the feedback it receives, to model for instance the relay of a signal from primary to higher cortical areas. For a given coupling architecture, the delays introduce correlations in the time series at the time-scale of the delay. It was found that the middle neuron leads the outer ones by the delay time, while the outer neurons are synchronized with zero lag times. Synchronization is found to be highly dependent on the synaptic time constant, with faster synapses increasing both the degree of synchronization and the firing rate. Analysis shows that presynaptic input during the interspike interval stabilizes the synchronous state, even for arbitrarily weak coupling, and independent of the initial phase. The finding may be of significance to synchronization of large groups of cells in the cortex that are spatially distanced from each other.Comment: 21 pages, 11 figure

Robust formation of morphogen gradients

We discuss the formation of graded morphogen profiles in a cell layer by nonlinear transport phenomena, important for patterning developing organisms. We focus on a process termed transcytosis, where morphogen transport results from binding of ligands to receptors on the cell surface, incorporation into the cell and subsequent externalization. Starting from a microscopic model, we derive effective transport equations. We show that, in contrast to morphogen transport by extracellular diffusion, transcytosis leads to robust ligand profiles which are insensitive to the rate of ligand production