Development of a Science Database System Applicable to Various Access Restrictions

金沢大学総合メディア基盤センターWe developed a general-purpose database (DB) system that manages and opens experimental and/or observational data accumulated in universities and academic institutes. This platform works as a web-DB management system in which databases can be easily managed without special skills and facilities. By defining a group manager and data manager, the proposed system defines a flexible access restriction for each user and each unit of datasets under the control of these managers. We demonstrate how a variety of web-DBs are appropriately integrated under one management system in such situations in which each web-DB has a different user interface in its search and data distribution functions and is designed with a different language (or script) and connection method to its DB. In spite of the diversity of web-DBs, the proposed system is highly suitable for practical use

Development of grid frameworks for clinical trials and epidemiological studies

E-Health initiatives such as electronic clinical trials and epidemiological studies require access to and usage of a range of both clinical and other data sets. Such data sets are typically only available over many heterogeneous domains where a plethora of often legacy based or in-house/bespoke IT solutions exist. Considerable efforts and investments are being made across the UK to upgrade the IT infrastructures across the National Health Service (NHS) such as the National Program for IT in the NHS (NPFIT) [1]. However, it is the case that currently independent and largely non-interoperable IT solutions exist across hospitals, trusts, disease registries and GP practices – this includes security as well as more general compute and data infrastructures. Grid technology allows issues of distribution and heterogeneity to be overcome, however the clinical trials domain places special demands on security and data which hitherto the Grid community have not satisfactorily addressed. These challenges are often common across many studies and trials hence the development of a re-usable framework for creation and subsequent management of such infrastructures is highly desirable. In this paper we present the challenges in developing such a framework and outline initial scenarios and prototypes developed within the MRC funded Virtual Organisations for Trials and Epidemiological Studies (VOTES) project [2]

Next generation software environments : principles, problems, and research directions

The past decade has seen a burgeoning of research and development in software environments. Conferences have been devoted to the topic of practical environments, journal papers produced, and commercial systems sold. Given all the activity, one might expect a great deal of consensus on issues, approaches, and techniques. This is not the case, however. Indeed, the term "environment" is still used in a variety of conflicting ways. Nevertheless substantial progress has been made and we are at least nearing consensus on many critical issues.The purpose of this paper is to characterize environments, describe several important principles that have emerged in the last decade or so, note current open problems, and describe some approaches to these problems, with particular emphasis on the activities of one large-scale research program, the Arcadia project. Consideration is also given to two related topics: empirical evaluation and technology transition. That is, how can environments and their constituents be evaluated, and how can new developments be moved effectively into the production sector

Mare Geneticum : Balancing Governance of Marine Genetic Resources in International Waters

Peer reviewedPublisher PD

A study to examine the operation and function of a virtual UK environmental specimen bank (UK-ESB). Final report

Executive Summary: 1. Environmental specimen banking is recognised internationally as an integral part of long-term environmental research and monitoring. Analysis of preserved environmental samples is often needed to detect and quantify patterns and rate of environmental change, and the emergence and progression of environmental hazards and risks. 2. National Environmental Specimen Banks have been established in several countries; they vary in scope and breadth. There are a few specialised environmental specimen holdings in the UK but no national-scale catalogue of holdings, despite an estimated annual spend of £16 million to store specimens. This lack of information results in under-exploitation of archived specimens and is a lost opportunity to facilitate world-class science and identify emerging pressures and threats on the environment. 3. An earlier project had identified key stakeholder organisations either engaged in archiving nationally important environmental specimens or who wished to utilise such specimens. These stakeholders had agreed there was a need for a national metadata catalogue of environmental specimens (subsequently termed a virtual UK-ESB). The objective of the current project was to further develop a virtual UK-ESB. Specifically, the aim was to work with stakeholders to establish the correct metadata entry fields, the search capabilities, the functionality and the nature of the hosting website of a virtual UK-ESB. 4. More than 80 stakeholder organisations that had previously expressed an interest in a UK-ESB were approached to provide feedback either electronically or by attending a stakeholder workshop. Thirty eight organisations responded. All remained interested in the UK-ESB concept and seventeen answered the survey questions. 5. Mock-ups of data entry screens, search screens and ideas around the functionality of a UK-ESB were developed by the CEH project team. These were mailed to stakeholders for feedback. Initial feedback was incorporated into the mock-ups which were then presented for discussion at a workshop comprising 15 attendees from across the specimen archiving community, CEH and the UK-EOF. 6. Workshop participants reviewed and agreed the format of 23 mandatory or optional data-entry fields for a virtual UK-ESB that, in the absence of standard for material samples and archives, were aligned with ISO19115 (geospatial metadata standard) and DublinCore (metadata standard). These fields were sub-divided into the following headings: Sample description, Categorisation, keywords and links, Storage Information and Contact information. Workshop participants also made a number of recommendations as to the format of the data entry screens and inclusion of extra fields. 7. Workshop participants reviewed options for search capabilities and made recommendations as to simple and advanced searching methods and their formats. It was also recommended that search facilities of the ESBs of other countries be examined to determine what is used, ease of use, and how they match the recommendations from the workshop. 8. Workshop participants reviewed options for functionality and agreed a detailed list of prioritised requirements. 9. Workshop participants agreed that a virtual UK-ESB should be hosted through a dedicated website that would also provide wider information, such as recently updated or added specimen holdings, most downloaded information, links to other groups, standard operating procedures, etc. 10. The next step for the development of a virtual UK-ESB is to implement the design and development ideas captured in the current report and build a test version of a virtual UK-ESB. This would be tested and refined, and could then be launched on a specifically designed website. This would need to be accompanied by a communication strategy. There is potential to link and co-brand a virtual UK-ESB with the UK-Environmental Observation Framework (UK-EOF)

RIVPACS database documentation. Final report

With the advent of the EU Water Framework Directive the concept of the 'reference condition' has become explicit within the legislative framework of the European Union. Reference condition has been established as a quality standard against which assessments of biological degradation must be compared. It is therefore essential that Member States can demonstrate that the biological datasets used to define their reference conditions meet the criteria of the WFD. The RIVPACS reference site dataset is therefore central to the definition of reference conditions for macroinvertebrates in streams and rivers in the United Kingdom. Objectives of research: • To establish the ownership of the RIVPACS reference site dataset • To liaise with all stakeholders of the dataset to establish unhindered access to the RIVPACS reference site dataset for the UK agencies (in perpetuity) • To deliver the RIVPACS reference site dataset to the UK agencies and to the public domain in a readily accessible database together will its accompanying physicochemical variables (both existing and newly collated as part of this project), historical and current anthropogenic stress data, and a range of calculated biotic indices. Key findings and recommendations: Ownership of the RIVPACS dataset resides with no single organization and several different organizations consider that they own different portions of the dataset. Formal permissions to release the dataset into the public domain have been obtained from all twelve extant organizations that have been identified as having funded various phases of RIVPACS research. In addition, CEH/NERC has also agreed to release the RIVPACS dataset to the public domain. Terms and conditions relating to the end use of the RIVPACS dataset have now been established. The RIVPACS database has been assembled in Microsoft® Access and can now be downloaded from the CEH web site. This report details the terms and conditions that apply to all end users of the database and it documents the tables given in the database, their structure and the origin of their data. A separate Pressure Data Analysis report describes the screening of the RIVPACS sites in terms of the current and emerging definitions of reference condition

The ALADIN Interactive Sky Atlas

The Aladin interactive sky atlas, developed at CDS, is a service providing simultaneous access to digitized images of the sky, astronomical catalogues, and databases. The driving motivation is to facilitate direct, visual comparison of observational data at any wavelength with images of the optical sky, and with reference catalogues. The set of available sky images consists of the STScI Digitized Sky Surveys, completed with high resolution images of crowded regions scanned at the MAMA facility in Paris. A Java WWW interface to the system is available at: http://aladin.u-strasbg.fr/Comment: 8 pages, 3 Postscript figures; to be published in A&