From access and integration to mining of secure genomic data sets across the grid

The UK Department of Trade and Industry (DTI) funded BRIDGES project (Biomedical Research Informatics Delivered by Grid Enabled Services) has developed a Grid infrastructure to support cardiovascular research. This includes the provision of a compute Grid and a data Grid infrastructure with security at its heart. In this paper we focus on the BRIDGES data Grid. A primary aim of the BRIDGES data Grid is to help control the complexity in access to and integration of a myriad of genomic data sets through simple Grid based tools. We outline these tools, how they are delivered to the end user scientists. We also describe how these tools are to be extended in the BBSRC funded Grid Enabled Microarray Expression Profile Search (GEMEPS) to support a richer vocabulary of search capabilities to support mining of microarray data sets. As with BRIDGES, fine grain Grid security underpins GEMEPS

An Examination of Technology Strategies for the Integration of Bioinformatics in Pharmaceutical R&D Processes

Bioinformatics is the use of computers for the storage, recall and analysis of data derived from scientific research aimed at providing answers to biological questions. Increasingly pharmaceutical firms are choosing to incorporate bioinformatics into their drug research and development (R&D) programs. Based on examination of recent literature and case studies of a cross section of the pharmaceutical industry and research community, this research concludes the following key points: Bioinformatics has been widely accepted as a new core competency for pharmaceutical research. Pharmaceutical firms are broadening their competencies to different extents to access new technologies. Integrated bioinformatics systems are systemic innovations and require strong in-house capabilities, however bioinformatics tools may also be used in an autonomous manner. Thus two groups of industrial users are emerging: those who use bioinformatics tools piecemeal and those who are attempting to integrate these tools into systems. Integration poses a complex set of technical and organisational problems, but may enable high throughput programs for drug discovery that optimise resources more effectively and thus provide competitive advantages. Such integrated systems must be tailor-made and are possible only through gaining competencies that are difficult to replicate. Additionally in this study theoretical frameworks are used to map technological change in the pharmaceutical process, showing how barriers to innovation and limiting steps within the R&D process are changing as a result of bioinformatics.bioinformatics, pharmaceutical industry, R&D, research and development, innovation

Paths Explored, Paths Omitted, Paths Obscured: Decision Points & Selective Reporting in End-to-End Data Analysis

Drawing reliable inferences from data involves many, sometimes arbitrary, decisions across phases of data collection, wrangling, and modeling. As different choices can lead to diverging conclusions, understanding how researchers make analytic decisions is important for supporting robust and replicable analysis. In this study, we pore over nine published research studies and conduct semi-structured interviews with their authors. We observe that researchers often base their decisions on methodological or theoretical concerns, but subject to constraints arising from the data, expertise, or perceived interpretability. We confirm that researchers may experiment with choices in search of desirable results, but also identify other reasons why researchers explore alternatives yet omit findings. In concert with our interviews, we also contribute visualizations for communicating decision processes throughout an analysis. Based on our results, we identify design opportunities for strengthening end-to-end analysis, for instance via tracking and meta-analysis of multiple decision paths

Simple identification tools in FishBase

Simple identification tools for fish species were included in the FishBase information system from its inception. Early tools made use of the relational model and characters like fin ray meristics. Soon pictures and drawings were added as a further help, similar to a field guide. Later came the computerization of existing dichotomous keys, again in combination with pictures and other information, and the ability to restrict possible species by country, area, or taxonomic group. Today, www.FishBase.org offers four different ways to identify species. This paper describes these tools with their advantages and disadvantages, and suggests various options for further development. It explores the possibility of a holistic and integrated computeraided strategy

Publish or patent?: Knowledge dissemination in agricultural biotechnology

"Plant transformation research has achieved outstanding progress in the development of transgenic crops over the past decades, and the research results have been spread through journal publications and patents. With the recent emergence of stronger intellectual property rights, investments in crop research and the landscape of plant transformation research have changed, along with the patterns of knowledge dissemination. In this paper, we discuss the recent trends in plant transformation research by examining patent and journal publication data during the last decade. The data analysis shows that there have been significant shifts toward applied research by developing countries and toward patenting as a means of knowledge dissemination during the past few decades, reflecting the increasing role of the private sector in developing countries in crop improvement research." from authors' abstractBiotechnology research, patents, Crop improvement, Science and technology, Genetic resources, Biodiversity, Journal publication, Developing countries,