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

Security-oriented data grids for microarray expression profiles

Microarray experiments are one of the key ways in which gene activity can be identified and measured thereby shedding light and understanding for example on biological processes. The BBSRC funded Grid enabled Microarray Expression Profile Search (GEMEPS) project has developed an infrastructure which allows post-genomic life science researchers to ask and answer the following questions: who has undertaken microarray experiments that are in some way similar or relevant to mine; and how similar were these relevant experiments? Given that microarray experiments are expensive to undertake and may possess crucial information for future exploitation (both academically and commercially), scientists are wary of allowing unrestricted access to their data by the wider community until fully exploited locally. A key requirement is thus to have fine grained security that is easy to establish and simple (or ideally transparent) to use across inter-institutional virtual organisations. In this paper we present an enhanced security-oriented data Grid infrastructure that supports the definition of these kinds of queries and the analysis and comparison of microarray experiment results

Learning Points and Routes to Recommend Trajectories

The problem of recommending tours to travellers is an important and broadly studied area. Suggested solutions include various approaches of points-of-interest (POI) recommendation and route planning. We consider the task of recommending a sequence of POIs, that simultaneously uses information about POIs and routes. Our approach unifies the treatment of various sources of information by representing them as features in machine learning algorithms, enabling us to learn from past behaviour. Information about POIs are used to learn a POI ranking model that accounts for the start and end points of tours. Data about previous trajectories are used for learning transition patterns between POIs that enable us to recommend probable routes. In addition, a probabilistic model is proposed to combine the results of POI ranking and the POI to POI transitions. We propose a new F$_1$ score on pairs of POIs that capture the order of visits. Empirical results show that our approach improves on recent methods, and demonstrate that combining points and routes enables better trajectory recommendations

Supporting security-oriented, collaborative nanoCMOS electronics research

Grid technologies support collaborative e-Research typified by multiple institutions and resources seamlessly shared to tackle common research problems. The rules for collaboration and resource sharing are commonly achieved through establishment and management of virtual organizations (VOs) where policies on access and usage of resources by collaborators are defined and enforced by sites involved in the collaboration. The expression and enforcement of these rules is made through access control systems where roles/privileges are defined and associated with individuals as digitally signed attribute certificates which collaborating sites then use to authorize access to resources. Key to this approach is that the roles are assigned to the right individuals in the VO; the attribute certificates are only presented to the appropriate resources in the VO; it is transparent to the end user researchers, and finally that it is manageable for resource providers and administrators in the collaboration. In this paper, we present a security model and implementation improving the overall usability and security of resources used in Grid-based e-Research collaborations through exploitation of the Internet2 Shibboleth technology. This is explored in the context of a major new security focused project at the National e-Science Centre (NeSC) at the University of Glasgow in the nanoCMOS electronics domain

Tool support for security-oriented virtual research collaborations

Collaboration is at the heart of e-Science and e-Research more generally. Successful collaborations must address both the needs of the end user researchers and the providers that make resources available. Usability and security are two fundamental requirements that are demanded by many collaborations and both concerns must be considered from both the researcher and resource provider perspective. In this paper we outline tools and methods developed at the National e-Science Centre (NeSC) that provide users with seamless, secure access to distributed resources through security-oriented research environments, whilst also allowing resource providers to define and enforce their own local access and usage policies through intuitive user interfaces. We describe these tools and illustrate their application in the ESRC-funded Data Management through e-Social Science (DAMES) and the JISC-funded SeeGEO projects

Data management of nanometre­ scale CMOS device simulations

In this paper we discuss the problems arising in managing and curating the data generated by simulations of nanometre scale CMOS (Complementary Metal–Oxide Semiconductor) transistors, circuits and systems and describe the software and operational techniques we have adopted to address them. Such simulations pose a number of challenges including, inter alia, multi­TByte data volumes, complex datasets with complex inter-relations between datasets, multi­-institutional collaborations including multiple specialisms and a mixture of academic and industrial partners, and demanding security requirements driven by commercial imperatives. This work was undertaken as part of the NanoCMOS project. However, the problems, solutions and experience seem likely to be of wider relevance, both within the CMOS design community and more generally in other disciplines

Grid infrastructures for the electronics domain: requirements and early prototypes from an EPSRC pilot project

The fundamental challenges facing future electronics design is to address the decreasing – atomistic - scale of transistor devices and to understand and predict the impact and statistical variability these have on design of circuits and systems. The EPSRC pilot project “Meeting the Design Challenges of nanoCMOS Electronics” (nanoCMOS) which began in October 2006 has been funded to explore this space. This paper outlines the key requirements that need to be addressed for Grid technology to support the various research strands in this domain, and shows early prototypes demonstrating how these requirements are being addressed

Secure, performance-oriented data management for nanoCMOS electronics

The EPSRC pilot project Meeting the Design Challenges of nanoCMOS Electronics (nanoCMOS) is focused upon delivering a production level e-Infrastructure to meet the challenges facing the semiconductor industry in dealing with the next generation of ‘atomic-scale’ transistor devices. This scale means that previous assumptions on the uniformity of transistor devices in electronics circuit and systems design are no longer valid, and the industry as a whole must deal with variability throughout the design process. Infrastructures to tackle this problem must provide seamless access to very large HPC resources for computationally expensive simulation of statistic ensembles of microscopically varying physical devices, and manage the many hundreds of thousands of files and meta-data associated with these simulations. A key challenge in undertaking this is in protecting the intellectual property associated with the data, simulations and design process as a whole. In this paper we present the nanoCMOS infrastructure and outline an evaluation undertaken on the Storage Resource Broker (SRB) and the Andrew File System (AFS) considering in particular the extent that they meet the performance and security requirements of the nanoCMOS domain. We also describe how metadata management is supported and linked to simulations and results in a scalable and secure manner

Supporting security-oriented, inter-disciplinary research: crossing the social, clinical and geospatial domains

How many people have had a chronic disease for longer than 5-years in Scotland? How has this impacted upon their choices of employment? Are there any geographical clusters in Scotland where a high-incidence of patients with such long-term illness can be found? How does the life expectancy of such individuals compare with the national averages? Such questions are important to understand the health of nations and the best ways in which health care should be delivered and measured for their impact and success. In tackling such research questions, e-Infrastructures need to provide tailored, secure access to an extensible range of distributed resources including primary and secondary e-Health clinical data; social science data, and geospatial data sets amongst numerous others. In this paper we describe the security models underlying these e-Infrastructures and demonstrate their implementation in supporting secure, federated access to a variety of distributed and heterogeneous data sets exploiting the results of a variety of projects at the National e-Science Centre (NeSC) at the University of Glasgow

GPs’ perspectives on the management of patients with multimorbidity: Systematic review and synthesis of qualitative research

Objective: To synthesise the existing published literature on the perceptions of general practitioners (GPs) or their equivalent on the clinical management of multimorbidity and determine targets for future research that aims to improve clinical care in multimorbidity. Design: Systematic review and metaethnographic synthesis of primary studies that used qualitative methods to explore GPs’ experiences of clinical management of multimorbidity or multiple chronic diseases. Data sources: EMBASE, MEDLINE, CINAHL, PsycInfo, Academic Search Complete, SocIndex, Social Science Full Text and digital theses/online libraries (database inception to September 2012) to identify literature using qualitative methods (focus groups or interviews). Review methods: The 7-step metaethnographic approach described by Noblit and Hare, which involves cross-interpretation between studies while preserving the context of the primary data. Results: Of 1805 articles identified, 37 were reviewed in detail and 10 were included, using a total of 275 GPs in 7 different countries. Four areas of difficulty specific to the management of multimorbidity emerged from these papers: disorganisation and fragmentation of healthcare; the inadequacy of guidelines and evidence-based medicine; challenges in delivering patient-centred care; and barriers to shared decision-making. A ‘line of argument’ was drawn which described GPs’ sense of isolation in decision-making for multimorbid patients. Conclusions: This systematic review shows that the problem areas for GPs in the management of multimorbidity may be classified into four domains. There will be no ‘one size fits all’ intervention for multimorbidity but these domains may be useful targets to guide the development of interventions that will assist and improve the provision of care to multimorbid patients