Computing and Information Systems - Research Publications
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ItemBioNessie: a grid enabled biochemical networks simulation environment(HealthGrid, 2008)The simulation of biochemical networks provides insight and understanding about the underlying biochemical processes and pathways used by cells and organisms. BioNessie is a biochemical network simulator which has been developed at the University of Glasgow. This paper describes the simulator and focuses in particular on how it has been extended to benefit from a wide variety of high performance compute resources across the UK through Grid technologies to support larger scale simulations.
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ItemE-infrastructures fostering multi-centre collaborative research into the intensive care management of patients with brain injury(Information Science Reference (an imprint of IGI Global), 2009)Clinical research is becoming ever more collaborative with multi-centre trials now a common practice. With this in mind, never has it been more important to have secure access to data and, in so doing, tackle the challenges of inter-organisational data access and usage. This is especially the case for research conducted within the brain injury domain due to the complicated multi-trauma nature of the disease with its associated complex collation of time-series data of varying resolution and quality. It is now widely accepted that advances in treatment within this group of patients will only be delivered if the technical infrastructures underpinning the collection and validation of multi-centre research data for clinical trials is improved. In recognition of this need, IT-based multi-centre e-Infrastructures such as the Brain Monitoring with Information Technology group (BrainIT - www.brainit.org) and Cooperative Study on Brain Injury Depolarisations (COSBID - www.cosbid.de) have been formed. A serious impediment to the effective implementation of these networks is access to the know-how and experience needed to install, deploy and manage security-oriented middleware systems that provide secure access to distributed hospital based datasets and especially the linkage of these data sets across sites. The recently funded EU framework VII ICT project Advanced Arterial Hypotension Adverse Event prediction through a Novel Bayesian Neural Network (AVERT-IT) is focused upon tackling these challenges. This chapter describes the problems inherent to data collection within the brain injury medical domain, the current IT-based solutions designed to address these problems and how they perform in practice. The authors outline how the authors have collaborated towards developing Grid solutions to address the major technical issues. Towards this end we describe a prototype solution which ultimately formed the basis for the AVERT-IT project. They describe the design of the underlying Grid infrastructure for AVERT-IT and how it will be used to produce novel approaches to data collection, data validation and clinical trial design.
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ItemSupporting the clinical trial recruitment process through the grid(NATL E-SCIENCE CENTRE, 2006)
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ItemBioNessie: a grid enabled biochemical networks simulation environment(IOS Press, 2008)The simulation of biochemical networks provides insight and understanding about the underlying biochemical processes and pathways used by cells and organisms. BioNessie is a biochemical network simulator which has been developed at the University of Glasgow. This paper describes the simulator and focuses in particular on how it has been extended to benefit from a wide variety of high performance compute resources across the UK through Grid technologies to support larger scale simulations.
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ItemGrid infrastructures supporting paediatric endocrinology across Europe(National e-Science Centre, 2007)Paediatric endocrinology is a highly specialised area of clinical medicine with many experts with specific knowledge distributed over a wide geographical area. The European Society for Paediatric Endocrinology (ESPE) is an example of such a body of experts that require regular collaboration and sharing of data and knowledge. This paper describes work, developed as a corollary to the VOTES project [1] and implementing similar architectures, to provide a data grid that allows information to be efficiently distributed between collaborating partners, and also allows wide-scale analyses to be run over the entire data-set, which necessarily involves crossing domain boundaries and negotiating data access between administrations that only trust each other to a limited degree.
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ItemExperiences of applying advanced grid authorisation infrastructures(Springer, 2005)The widespread acceptance and uptake of Grid technology can only be achieved if it can be ensured that the security mechanisms needed to support Grid based collaborations are at least as strong as local security mechanisms. The predominant way in which security is currently addressed in the Grid community is through Public Key Infrastructures (PKI) to support authentication. Whilst PKIs address user identity issues, authentication does not provide fine grained control over what users are allowed to do on remote resources (authorisation). The Grid community have put forward numerous software proposals for authorisation infrastructures such as AKENTI [1], CAS [2], CARDEA [3], GSI [4], PERMIS [5,6,7] and VOMS [8,9]. It is clear that for the foreseeable future a collection of solutions will be the norm. To address this, the Global Grid Forum (GGF) have proposed a generic SAML based authorisation API which in principle should allow for fine grained control for authorised access to any Grid service. Experiences in applying and stress testing this API from a variety of different application domains are essential to give insight into the practical aspects of large scale usage of authorisation infrastructures. This paper presents experiences from the DTI funded BRIDGES project [10] and the JISC funded DyVOSE project [11] in using this API with Globus version 3.3 [12] and the PERMIS authorisation infrastructure.