David Thorne

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

WIWS: a protein structure bioinformatics Web service collection

The WHAT IF molecular-modelling and drug design program is widely distributed in the world of protein structure bioinformatics. Although originally designed as an interactive application, its highly modular design and inbuilt control language have recently enabled its deployment as a collection of programmatically accessible web services. We report here a collection of WHAT IF-based protein structure bioinformatics web services: these relate to structure quality, the use of symmetry in crystal structures, structure correction and optimization, adding hydrogens and optimizing hydrogen bonds and a series of geometric calculations. The freely accessible web services are based on the industry standard WS-I profile and the EMBRACE technical guidelines, and are available via both REST and SOAP paradigms. The web services run on a dedicated computational cluster; their function and availability is monitored daily.

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/.

An active registry for bioinformatics web services

Summary: The EMBRACE Registry is a web portal that collects and monitors web services according to test scripts provided by the their administrators. Users are able to search for, rank and annotate services, enabling them to select the most appropriate working service for inclusion in their bioinformatics analysis tasks. Availability and implementation: Web site implemented with PHP, Python, MySQL and Apache, with all major browsers supported. (www.embraceregistry.net) Contact: steve.pettifer@manchester.ac.uk

NucleaRDB: information system for nuclear receptors

The NucleaRDB is a Molecular Class-Specific Information System that collects, combines, validates and disseminates large amounts of heterogeneous data on nuclear hormone receptors. It contains both experimental and computationally derived data. The data and knowledge present in the NucleaRDB can be accessed using a number of different interactive and programmatic methods and query systems. A nuclear hormone receptor-specific PDF reader interface is available that can integrate the contents of the NucleaRDB with full-text scientific articles. The NucleaRDB is freely available at http://www.receptors.org/nucleardb.

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.

Reuniting data and narrative in scientific articles

Data and narrative are both important for scientific discourse. They are ‘united’ in the mind of the scientist-author, yet the current publishing process favours narrative at the expense of data, making it hard to recreate experiments, intuitively link to relevant data points outside the article in question, or indeed find associated data sets. Utopia Documents helps to solve this problem by enabling readers of articles to follow leads without the need to flip (and particularly search) through other systems, and so enhances their ability to gain a deeper understanding of the arguments being presented. Utopia Documents also removes the linkability barriers hitherto inherent in the PDF format, by bridging the connection gap with the web.