A Linked Data Approach to Sharing Workflows and Workflow Results

A bioinformatics analysis pipeline is often highly elaborate, due to the inherent complexity of biological systems and the variety and size of datasets. A digital equivalent of the ‘Materials and Methods’ section in wet laboratory publications would be highly beneficial to bioinformatics, for evaluating evidence and examining data across related experiments, while introducing the potential to find associated resources and integrate them as data and services. We present initial steps towards preserving bioinformatics ‘materials and methods’ by exploiting the workflow paradigm for capturing the design of a data analysis pipeline, and RDF to link the workflow, its component services, run-time provenance, and a personalized biological interpretation of the results. An example shows the reproduction of the unique graph of an analysis procedure, its results, provenance, and personal interpretation of a text mining experiment. It links data from Taverna, myExperiment.org, BioCatalogue.org, and ConceptWiki.org. The approach is relatively ‘light-weight’ and unobtrusive to bioinformatics users

Requirements for In-Situ Authoring of Location Based Experiences

In this paper we describe an investigation into the requirements for and the use of in-situ authoring in the creation of location based pervasive and UbiComp experiences. We will focus on the co-design process with users that resulted in a novel visitor experience to a historic country estate. This has informed the design of new, in-situ, authoring tools supplemented with tools for retrospective revisiting and reorganization of content. An initial trial of these new tools will be discussed and conclusions drawn as to the appropriateness of such tools. Further enhancements as part of future trials will also be described

Iron Behaving Badly: Inappropriate Iron Chelation as a Major Contributor to the Aetiology of Vascular and Other Progressive Inflammatory and Degenerative Diseases

The production of peroxide and superoxide is an inevitable consequence of aerobic metabolism, and while these particular "reactive oxygen species" (ROSs) can exhibit a number of biological effects, they are not of themselves excessively reactive and thus they are not especially damaging at physiological concentrations. However, their reactions with poorly liganded iron species can lead to the catalytic production of the very reactive and dangerous hydroxyl radical, which is exceptionally damaging, and a major cause of chronic inflammation. We review the considerable and wide-ranging evidence for the involvement of this combination of (su)peroxide and poorly liganded iron in a large number of physiological and indeed pathological processes and inflammatory disorders, especially those involving the progressive degradation of cellular and organismal performance. These diseases share a great many similarities and thus might be considered to have a common cause (i.e. iron-catalysed free radical and especially hydroxyl radical generation). The studies reviewed include those focused on a series of cardiovascular, metabolic and neurological diseases, where iron can be found at the sites of plaques and lesions, as well as studies showing the significance of iron to aging and longevity. The effective chelation of iron by natural or synthetic ligands is thus of major physiological (and potentially therapeutic) importance. As systems properties, we need to recognise that physiological observables have multiple molecular causes, and studying them in isolation leads to inconsistent patterns of apparent causality when it is the simultaneous combination of multiple factors that is responsible. This explains, for instance, the decidedly mixed effects of antioxidants that have been observed, etc...Comment: 159 pages, including 9 Figs and 2184 reference

The Semantic Grid: Past, Present and Future.

Grid computing offers significant enhancements to our capabilities for computation, information processing and collaboration, and has exciting ambitions in many fields of endeavour. This talk will explain why the full richness of the Grid vision, with its application in e-Science, e-Research or e-Business, requires the combination of Semantic Web and Grid - giving us the "Semantic Grid", an extension of the current Grid in which information and services are given well-defined meaning, better enabling computers and people to work in cooperation. The history and state of the art in Semantic Grid will be presented, and future trends discussed. © Springer-Verlag Berlin Heidelberg 2005

Machines, methods and music: On the evolution of e-Research.

Against a backdrop of increasing computational capability we are seeing acceleration of research through broader adoption and sharing of tools, techniques and resources, both for big science and the long tail scientist. This paper discusses the evolution of e-Research, focusing on a web-scale computational musicology project as an illustration of emerging methodology and using the myExperiment social website as a lens to glimpse future research practice. © 2011 IEEE

Hypermedia by coincidence.

An approach to linking hypermedia documents dynamically in a decentralized, peer-to-peer manner using resources that were available by coincidence was introduced without explicit configuration. The approach presented utilized an open platform in combination with distributed link service technology enabling dynamic hypertext generation. It was discovered that the critical hypermedia applications issue, during introducing hypermedia services was the way to resolve uniform resource locator (URL) to local copies or representations of the resource in a meaningful way

Machines, methods and music: On the evolution of e-Research.

Against a backdrop of increasing computational capability we are seeing acceleration of research through broader adoption and sharing of tools, techniques and resources, both for big science and the long tail scientist. This paper discusses the evolution of e-Research, focusing on a web-scale computational musicology project as an illustration of emerging methodology and using the myExperiment social website as a lens to glimpse future research practice. © 2011 IEEE