Stephen Pettifer

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

Arcadia: a visualization tool for metabolic pathways

Summary: Arcadia translates text-based descriptions of biological networks (SBML files) into standardized diagrams (SBGN PD maps). Users can view the same model from different perspectives and easily alter the layout to emulate traditional textbook representations. Availability and Implementation: Arcadia is written in C++. The source code is available (along with Mac OS and Windows binaries) under the GPL from http://arcadiapathways.sourceforge.net/ Contact: alice.villeger@manchester.ac.uk Supplementary information: Supplementary data are available at Bioinformatics online.

Investigating the efficacy of a virtual mirror box in treating phantom limb pain in a sample of chronic sufferers.

This paper describes a pilot clinical study to evaluate the efficacy of using immersive virtual reality (IVR) as a rehabilitative technology for phantom limb pain experienced by amputees. This work builds upon prior research which has used simple devices such as the mirror box (where the amputee sees a mirror image of their remaining anatomical limb in the phenomenal space of their amputated limb) to induce vivid sensations of movement originating from the muscles and joints of their phantom limb and to relieve pain. The IVR system transposes movements of amputees’ anatomical limbs into movements of a virtual limb which is presented in the phenomenal space of their phantom limb. The primary focus here is on a qualitative analysis of interview data with each participant throughout the study. We argue that the findings of this work make a case for proof of principle for this approach for phantom pain treatment.