Grid infrastructures for secure access to and use of bioinformatics data: experiences from the BRIDGES project

The BRIDGES project was funded by the UK Department of Trade and Industry (DTI) to address the needs of cardiovascular research scientists investigating the genetic causes of hypertension as part of the Wellcome Trust funded (£4.34M) cardiovascular functional genomics (CFG) project. Security was at the heart of the BRIDGES project and an advanced data and compute grid infrastructure incorporating latest grid authorisation technologies was developed and delivered to the scientists. We outline these grid infrastructures and describe the perceived security requirements at the project start including data classifications and how these evolved throughout the lifetime of the project. The uptake and adoption of the project results are also presented along with the challenges that must be overcome to support the secure exchange of life science data sets. We also present how we will use the BRIDGES experiences in future projects at the National e-Science Centre

Application of Semantics to Solve Problems in Life Sciences

Fecha de lectura de Tesis: 10 de diciembre de 2018La cantidad de información que se genera en la Web se ha incrementado en los últimos años. La mayor parte de esta información se encuentra accesible en texto, siendo el ser humano el principal usuario de la Web. Sin embargo, a pesar de todos los avances producidos en el área del procesamiento del lenguaje natural, los ordenadores tienen problemas para procesar esta información textual. En este cotexto, existen dominios de aplicación en los que se están publicando grandes cantidades de información disponible como datos estructurados como en el área de las Ciencias de la Vida. El análisis de estos datos es de vital importancia no sólo para el avance de la ciencia, sino para producir avances en el ámbito de la salud. Sin embargo, estos datos están localizados en diferentes repositorios y almacenados en diferentes formatos que hacen difícil su integración. En este contexto, el paradigma de los Datos Vinculados como una tecnología que incluye la aplicación de algunos estándares propuestos por la comunidad W3C tales como HTTP URIs, los estándares RDF y OWL. Haciendo uso de esta tecnología, se ha desarrollado esta tesis doctoral basada en cubrir los siguientes objetivos principales: 1) promover el uso de los datos vinculados por parte de la comunidad de usuarios del ámbito de las Ciencias de la Vida 2) facilitar el diseño de consultas SPARQL mediante el descubrimiento del modelo subyacente en los repositorios RDF 3) crear un entorno colaborativo que facilite el consumo de Datos Vinculados por usuarios finales, 4) desarrollar un algoritmo que, de forma automática, permita descubrir el modelo semántico en OWL de un repositorio RDF, 5) desarrollar una representación en OWL de ICD-10-CM llamada Dione que ofrezca una metodología automática para la clasificación de enfermedades de pacientes y su posterior validación haciendo uso de un razonador OWL

Towards data grids for microarray expression profiles

The UK DTI funded Biomedical Research Informatics Delivered by Grid Enabled Services (BRIDGES) project developed a Grid infrastructure through which research into the genetic causes of hypertension could be supported by scientists within the large Wellcome Trust funded Cardiovascular Functional Genomics project. The BRIDGES project had a focus on developing a compute Grid and a data Grid infrastructure with security at its heart. Building on the work within BRIDGES, the BBSRC funded Grid enabled Microarray Expression Profile Search (GEMEPS) project plans to provide an enhanced data Grid infrastructure to support richer queries needed for the discovery and analysis of microarray data sets, also based upon a fine-grained security infrastructure. This paper outlines the experiences gained within BRIDGES and outlines the status of the GEMEPS project, the open challenges that remain and plans for the future

BlogForever D3.2: Interoperability Prospects

This report evaluates the interoperability prospects of the BlogForever platform. Therefore, existing interoperability models are reviewed, a Delphi study to identify crucial aspects for the interoperability of web archives and digital libraries is conducted, technical interoperability standards and protocols are reviewed regarding their relevance for BlogForever, a simple approach to consider interoperability in specific usage scenarios is proposed, and a tangible approach to develop a succession plan that would allow a reliable transfer of content from the current digital archive to other digital repositories is presented

A Critical Look at Decentralized Personal Data Architectures

While the Internet was conceived as a decentralized network, the most widely used web applications today tend toward centralization. Control increasingly rests with centralized service providers who, as a consequence, have also amassed unprecedented amounts of data about the behaviors and personalities of individuals. Developers, regulators, and consumer advocates have looked to alternative decentralized architectures as the natural response to threats posed by these centralized services. The result has been a great variety of solutions that include personal data stores (PDS), infomediaries, Vendor Relationship Management (VRM) systems, and federated and distributed social networks. And yet, for all these efforts, decentralized personal data architectures have seen little adoption. This position paper attempts to account for these failures, challenging the accepted wisdom in the web community on the feasibility and desirability of these approaches. We start with a historical discussion of the development of various categories of decentralized personal data architectures. Then we survey the main ideas to illustrate the common themes among these efforts. We tease apart the design characteristics of these systems from the social values that they (are intended to) promote. We use this understanding to point out numerous drawbacks of the decentralization paradigm, some inherent and others incidental. We end with recommendations for designers of these systems for working towards goals that are achievable, but perhaps more limited in scope and ambition

Built to Change: Catalytic Capacity-Building in Nonprofit Organizations

Summarizes the results of a broad survey of programs, and business and nonprofit experts, in the field of organizational effectiveness

The GLASS project: supporting secure shibboleth-based single sign-on to campus resources

Higher and Further education institutions in the UK are in the process of migrating their IT infrastructures to exploit Shibboleth technologies for federated access management. Ease of use and secure access are paramount to the successful uptake of these technologies, both from the end user and system administrator perspective. The JISC-funded GLASS project is a one-year project investigating the use of Shibboleth to support single sign-on to a variety of campus resources at the University of Glasgow including browser-based email access; the Moodle online virtual learning environment; the WebSURF online student records facility, and a network filestore browser. This paper describes the implementation issues and experiences gained in rolling out the Shibboleth technologies to support federated access management