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]

Innovative in silico approaches to address avian flu using grid technology

The recent years have seen the emergence of diseases which have spread very quickly all around the world either through human travels like SARS or animal migration like avian flu. Among the biggest challenges raised by infectious emerging diseases, one is related to the constant mutation of the viruses which turns them into continuously moving targets for drug and vaccine discovery. Another challenge is related to the early detection and surveillance of the diseases as new cases can appear just anywhere due to the globalization of exchanges and the circulation of people and animals around the earth, as recently demonstrated by the avian flu epidemics. For 3 years now, a collaboration of teams in Europe and Asia has been exploring some innovative in silico approaches to better tackle avian flu taking advantage of the very large computing resources available on international grid infrastructures. Grids were used to study the impact of mutations on the effectiveness of existing drugs against H5N1 and to find potentially new leads active on mutated strains. Grids allow also the integration of distributed data in a completely secured way. The paper presents how we are currently exploring how to integrate the existing data sources towards a global surveillance network for molecular epidemiology.Comment: 7 pages, submitted to Infectious Disorders - Drug Target

Grid-based semantic integration of heterogeneous data resources: Implementation on a HealthGrid

This thesis was submitted for the degree of Doctor of Philosophy and was awarded by Brunel University.The semantic integration of geographically distributed and heterogeneous data resources still remains a key challenge in Grid infrastructures. Today's mainstream Grid technologies hold the promise to meet this challenge in a systematic manner, making data applications more scalable and manageable. The thesis conducts a thorough investigation of the problem, the state of the art, and the related technologies, and proposes an Architecture for Semantic Integration of Data Sources (ASIDS) addressing the semantic heterogeneity issue. It defines a simple mechanism for the interoperability of heterogeneous data sources in order to extract or discover information regardless of their different semantics. The constituent technologies of this architecture include Globus Toolkit (GT4) and OGSA-DAI (Open Grid Service Architecture Data Integration and Access) alongside other web services technologies such as XML (Extensive Markup Language). To show this, the ASIDS architecture was implemented and tested in a realistic setting by building an exemplar application prototype on a HealthGrid (pilot implementation). The study followed an empirical research methodology and was informed by extensive literature surveys and a critical analysis of the relevant technologies and their synergies. The two literature reviews, together with the analysis of the technology background, have provided a good overview of the current Grid and HealthGrid landscape, produced some valuable taxonomies, explored new paths by integrating technologies, and more importantly illuminated the problem and guided the research process towards a promising solution. Yet the primary contribution of this research is an approach that uses contemporary Grid technologies for integrating heterogeneous data resources that have semantically different. data fields (attributes). It has been practically demonstrated (using a prototype HealthGrid) that discovery in semantically integrated distributed data sources can be feasible by using mainstream Grid technologies, which have been shown to have some Significant advantages over non-Grid based approaches

Initial experiences in developing e-health solutions across Scotland

The MRC funded Virtual Organisations for Trials and Epidemiological Studies (VOTES) project is a collaborative effort between e-Science, clinical and ethical research centres across the UK including the universities of Oxford, Glasgow, Imperial, Nottingham and Leicester. The project started in September 2005 and is due to run for 3 years. The primary goal of VOTES is to develop a reusable Grid framework through which a multitude of clinical trials and epidemiological studies can be supported. The National e-Science Centre (NeSC) at the University of Glasgow are looking at developing the Scottish components of this framework. This paper presents the initial experiences in developing this framework and in accessing and using existing data sets, services and software across the NHS in Scotland

User oriented access to secure biomedical resources through the grid

The life science domain is typified by heterogeneous data sets that are evolving at an exponential rate. Numerous post-genomic databases and areas of post-genomic life science research have been established and are being actively explored. Whilst many of these databases are public and freely accessible, it is often the case that researchers have data that is not so freely available and access to this data needs to be strictly controlled when distributed collaborative research is undertaken. Grid technologies provide one mechanism by which access to and integration of federated data sets is possible. Combining such data access and integration technologies with fine grained security infrastructures facilitates the establishment of virtual organisations (VO). However experience has shown that the general research (non-Grid) community are not comfortable with the Grid and its associated security models based upon public key infrastructures (PKIs). The Internet2 Shibboleth technology helps to overcome this through users only having to log in to their home site to gain access to resources across a VO – or in Shibboleth terminology a federation. In this paper we outline how we have applied the combination of Grid technologies, advanced security infrastructures and the Internet2 Shibboleth technology in several biomedical projects to provide a user-oriented model for secure access to and usage of Grid resources. We believe that this model may well become the de facto mechanism for undertaking e-Research on the Grid across numerous domains including the life sciences