James Marsh

Low-complexity regions within protein sequences have position-dependent roles.

BackgroundRegions of protein sequences with biased amino acid composition (so-called Low-Complexity Regions (LCRs)) are abundant in the protein universe. A number of studies have revealed that i) these regions show significant divergence across protein families; ii) the genetic mechanisms from which they arise lends them remarkable degrees of compositional plasticity. They have therefore proved difficult to compare using conventional sequence analysis techniques, and functions remain to be elucidated for most of them. Here we undertake a systematic investigation of LCRs in order to explore their possible functional significance, placed in the particular context of Protein-Protein Interaction (PPI) networks and Gene Ontology (GO)-term analysis.ResultsIn keeping with previous results, we found that LCR-containing proteins tend to have more binding partners across different PPI networks than proteins that have no LCRs. More specifically, our study suggests i) that LCRs are preferentially positioned towards the protein sequence extremities and, in contrast with centrally-located LCRs, such terminal LCRs show a correlation between their lengths and degrees of connectivity, and ii) that centrally-located LCRs are enriched with transcription-related GO terms, while terminal LCRs are enriched with translation and stress response-related terms.ConclusionsOur results suggest not only that LCRs may be involved in flexible binding associated with specific functions, but also that their positions within a sequence may be important in determining both their binding properties and their biological roles.

Utopia documents

Motivation: In recent years, the gulf between the mass of accumulating-research data and the massive literature describing and analyzing those data has widened. The need for intelligent tools to bridge this gap, to rescue the knowledge being systematically isolated in literature and data silos, is now widely acknowledged. Results: To this end, we have developed Utopia Documents, a novel PDF reader that semantically integrates visualization and data-analysis tools with published research articles. In a successful pilot with editors of the Biochemical Journal (BJ), the system has been used to transform static document features into objects that can be linked, annotated, visualized and analyzed interactively (http://www.biochemj.org/bj/424/3/). Utopia Documents is now used routinely by BJ editors to mark up article content prior to publication. Recent additions include integration of various text-mining and biodatabase plugins, demonstrating the systems ability to seamlessly integrate on-line content with PDF articles. Availability: http://getutopia.com Contact: teresa.k.attwood@manchester.ac.uk

A network architecture supporting consistent rich behavior in collaborative interactive applications

Network architectures for collaborative virtual reality have traditionally been dominated by client-server and peer-to-peer approaches, with peer-to-peer strategies typically being favored where minimizing latency is a priority and client-server where consistency is key. With increasingly sophisticated behavior models and the demand for better support for haptics, we argue that neither approach provides sufficient support for these scenarios nor, thus, a hybrid architecture is required. We discuss the relative performance of different distribution strategies in the face of real network conditions and illustrate the problems they face. Finally, we present an architecture that successfully meets many of these challenges and demonstrate its use in a distributed virtual prototyping application which supports simultaneous collaboration for assembly, maintenance, and training applications utilizing haptics

DEVA3: architecture for a large-scale distributed virtual reality system

In this paper we present work undertaken by the Advanced Interfaces Group at the University of Manchester on the design and development of a system to support large numbers of geographically distributed users in complex, large-scale virtual environments (VEs).We shown how the problem of synchronisation in the face of network limitations is being addressed by the Deva system through the exploitation of subjectivity. Further, we present a model for flexibly describing object behaviours in the VEs.Applications of the system in use are described.

Visualising biological data: A semantic approach to tool and database integration

MotivationIn the biological sciences, the need to analyse vast amounts of information has become commonplace. Such large-scale analyses often involve drawing together data from a variety of different databases, held remotely on the internet or locally on in-house servers. Supporting these tasks are ad hoc collections of data-manipulation tools, scripting languages and visualisation software, which are often combined in arcane ways to create cumbersome systems that have been customised for a particular purpose, and are consequently not readily adaptable to other uses. For many day-to-day bioinformatics tasks, the sizes of current databases, and the scale of the analyses necessary, now demand increasing levels of automation; nevertheless, the unique experience and intuition of human researchers is still required to interpret the end results in any meaningful biological way. Putting humans in the loop requires tools to support real-time interaction with these vast and complex data-sets. Numerous tools do exist for this purpose, but many do not have optimal interfaces, most are effectively isolated from other tools and databases owing to incompatible data formats, and many have limited real-time performance when applied to realistically large data-sets: much of the users cognitive capacity is therefore focused on controlling the software and manipulating esoteric file formats rather than on performing the research.MethodsTo confront these issues, harnessing expertise in human-computer interaction (HCI), high-performance rendering and distributed systems, and guided by bioinformaticians and end-user biologists, we are building reusable software components that, together, create a toolkit that is both architecturally sound from a computing point of view, and addresses both user and developer requirements. Key to the systems usability is its direct exploitation of semantics, which, crucially, gives individual components knowledge of their own functionality and allows them to interoperate seamlessly, removing many of the existing barriers and bottlenecks from standard bioinformatics tasks.ResultsThe toolkit, named Utopia, is freely available from http://utopia.cs.man.ac.uk/.

Ceci n'est pas un hamburger: Modelling and representing the scholarly article

Current approaches to publishing scholarly work are falling behind the growing demands of modern readers, who need easy access to the underlying data, as well as the ability to consume content on an ever‐growing variety of electronic devices. The pros and cons of the various formats for representing the scholarly article are hotly contested, but as yet these debates have had little tangible impact on the publishing world where, in spite of its apparent limitations, the PDF remains the dominant form of distribution. We discuss fundamental philosophical differences between a scholarly work and its representation, and describe Utopia Documents, which realizes those differences in software, aiming to resolve many of the current issues in this area.

myGrid and UTOPIA: an integrated approach to enacting and visualising in silico experiments in the life sciences

In silico experiments have hitherto required ad hoc collections of scripts and programs to process and visualise biological data, consuming substantial amounts of time and effort to build, and leading to tools that are difficult to use, are architecturally fragile and scale poorly. With examples of the systems applied to real biological problems, we describe two complimentary software frameworks that address this problem in a principled manner; myGrid/Taverna, a workflow design and enactment environment enabling coherent experiments to be built, and UTOPIA, a flexible visualisation system to aid in examining experimental results.

The importance of locality in the visualization of large datasets

Many scientific phenomena in large high‐resolution datasets such as the U.K. Ocean Circulation and Advanced Modelling (OCCAM) ocean model are better discovered through visualization than by algorithmic analysis: it is often more straightforward to see a feature than it is to characterize it numerically. Using traditional rendering techniques, the size of modern datasets presents a challenge for even high‐end graphical supercomputers, and the cost of such hardware limits its availability for day‐to‐day analysis. We present an architecture that brings visual analysis to the desktop by exploiting consumer‐grade graphics hardware in order to provide initial interactive exploration and Web services to enable finer‐grained analysis and interoperability with traditional visualization tools. Copyright

Minimising latency and maintaining consistency in distributed virtual prototyping

This paper describes a computer aided design tool for mechanical engineering applications, combining component assembly simulation, the modelling of rigid and flexible bodies and haptic interaction in a multi-user distributed virtual environment. It presents the research challenges encountered, and an architecture designed to address these.

GRENADE: a Grid Enabled Desktop Environment

Making grid technology available to a wider community requires moving away from the complex command line tools commonly in use today towards a more transparent and user-friendly interface. We seek to address this challenge by presenting the notion of a Grid Enabled Desktop Environment (GRENADE), seamlessly extending the familiar desktop user-interface paradigm to interactions with grid resources. This paper describes our initial implementation.