Development of usable grid services for the biomedical community

The BRIDGES project was funded by the UK Department of Trade and Industry to directly address the needs of the cardiovascular research scientists investigating the genetic causes of hypertension as part of the Wellcome Trust funded (£4.34M) Cardiovascular Functional Genomics (CFG) project. Specifically, the BRIDGES project developed a compute Grid and a data Grid with security at its heart. This paper presents the experiences in developing usable Grid services for the bio-community and the different phases of prototypes that were refined based upon user requirements and feedback

From access and integration to mining of secure genomic data sets across the grid

The UK Department of Trade and Industry (DTI) funded BRIDGES project (Biomedical Research Informatics Delivered by Grid Enabled Services) has developed a Grid infrastructure to support cardiovascular research. This includes the provision of a compute Grid and a data Grid infrastructure with security at its heart. In this paper we focus on the BRIDGES data Grid. A primary aim of the BRIDGES data Grid is to help control the complexity in access to and integration of a myriad of genomic data sets through simple Grid based tools. We outline these tools, how they are delivered to the end user scientists. We also describe how these tools are to be extended in the BBSRC funded Grid Enabled Microarray Expression Profile Search (GEMEPS) to support a richer vocabulary of search capabilities to support mining of microarray data sets. As with BRIDGES, fine grain Grid security underpins GEMEPS

Frameworks: the future of formal software development?

It could be argued that the primary issue to be dealt with in software engineering today is re-use of software. Current software development rarely, if ever, starts from nothing. Unfortunately, the same cannot be said for the development of specifications. To overcome this problem, various works have attempted to show how specifications can be built using architectural principles. We discuss one such approach in particular, the Architectural Semantics of Open Distributed Processing. We show the limitations of this work with regard to the architecting of specifications and propose a new approach, based on frameworks. To highlight the approach we use the work currently being done in the TOSCA project in its development of a service creation and validation environment for telecommunication services

The formal, tool supported development of real time systems

The language SDL has long been applied in the development of various kinds of systems. Real-time systems are one application area where SDL has been applied extensively. Whilst SDL allows for certain modelling aspects of real-time systems to be represented, the language and its associated tool support have certain drawbacks for modelling and reasoning about such systems. In this paper we highlight the limitations of SDL and its associated tool support in this domain and present language extensions and next generation real-time system tool support to help overcome them. The applicability of the extensions and tools is demonstrated through a case study based upon a multimedia binding object used to support a configuration of time dependent information producers and consumers realising the so called lip-synchronisation algorithm

Specifying multimedia configurations in Z

In this paper we illustrate how the formal specification language Z can be used to reason about the temporal and throughput constraints associated with multimedia flows of information. In particular we show how it is possible to specify issues related to maximum delays, throughputs and jitter of information flows and how control of these flows can be achieved. What makes our work particularly interesting is that we deal with temporal aspects of systems without the use of a temporal logic. Rather, we highlight the versatility of the Z language in modelling systems with real time constraints

E-infrastructures fostering multi-centre collaborative research into the intensive care management of patients with brain injury

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. We 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. We 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 is also presented

Finite state machine based SDL

No abstract available

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

Towards more accurate real time testing

The languages Message Sequence Charts (MSC) [1], System Design Language1 (SDL) [2] and Testing and Test Control Notation Testing2 (TTCN-3) [3] have been developed for the design, modelling and testing of complex software systems. These languages have been developed to complement one another in the software development process. Each of these languages has features for describing, analysing or testing the real time properties of systems. Robust toolsets exist which provide integrated environments for the design, analysis and testing of systems, and it is claimed, for the complete development of real time systems. It was shown in [4] however, that there are fundamental problems with the SDL language and its associated tools for modelling and reasoning about real time systems. In this paper we present the limitations of TTCN-3 and propose recommendations which help minimise the timing inaccuracies that would otherwise occur in using the language directly

Measuring Social Value Orientation

Narrow self-interest is often used as a simplifying assumption when studying people making decisions in social contexts. Nonetheless, people exhibit a wide range of different motivations when choosing unilaterally among interdependent outcomes. Measuring the magnitude of the concern people have for others, sometimes called Social Value Orientation (SVO), has been an interest of many social scientists for decades and several different measurement methods have been developed so far. Here we introduce a new measure of SVO that has several advantages over existent methods. A detailed description of the new measurement method is presented, along with norming data that provide evidence of its solid psychometric properties. We conclude with a brief discussion of the research streams that would benefit from a more sensitive and higher resolution measure of SVO, and extend an invitation to others to use this new measure which is freely availabl