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Publication History View all

  • Journal of Information Security and Applications. 01/2014;
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    ABSTRACT: The creation of a consistent system description is a challenging problem of requirements engineering. Formal and informal reasoning can greatly contribute to meet this challenge. However, this demands that formal and informal reasoning and the system ...
    Science of Computer Programming 01/2014; 82:1.
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    ABSTRACT: This paper describes the e-Science Central (e-SC) cloud data processing system and its application to a number of e-Science projects. e-SC provides both software as a service (SaaS) and platform as a service for scientific data management, analysis and collaboration. It is a portable system and can be deployed on both private (e.g. Eucalyptus) and public clouds (Amazon AWS and Microsoft Windows Azure). The SaaS application allows scientists to upload data, edit and run workflows and share results in the cloud, using only a Web browser. It is underpinned by a scalable cloud platform consisting of a set of components designed to support the needs of scientists. The platform is exposed to developers so that they can easily upload their own analysis services into the system and make these available to other users. A representational state transfer-based application programming interface (API) is also provided so that external applications can leverage the platform's functionality, making it easier to build scalable, secure cloud-based applications. This paper describes the design of e-SC, its API and its use in three different case studies: spectral data visualization, medical data capture and analysis, and chemical property prediction.
    Philosophical Transactions of The Royal Society A Mathematical Physical and Engineering Sciences 01/2013; 371(1983):20120085.
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    ABSTRACT: Event processing involves continuous evaluation of queries over streams of events. Response-time optimization is traditionally done over a fixed set of nodes and/or by using metrics measured at query-operator levels. Cloud computing makes it easy to acquire and release computing nodes as required. Leveraging this flexibility, we propose a novel, queueing-theory-based approach for meeting specified response-time targets against fluctuating event arrival rates by drawing only the necessary amount of computing resources from a cloud platform. In the proposed approach, the entire processing engine of a distinct query is modelled as an atomic unit for predicting response times. Several such units hosted on a single node are modelled as a multiple class M/G/1 system. These aspects eliminate intrusive, low-level performance measurements at run-time, and also offer portability and scalability. Using model-based predictions, cloud resources are efficiently used to meet response-time targets. The efficacy of the approach is demonstrated through cloud-based experiments.
    Philosophical Transactions of The Royal Society A Mathematical Physical and Engineering Sciences 01/2013; 371(1983):20120095.
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    ABSTRACT: BacillOndex is an extension of the Ondex data integration system, providing a semantically annotated, integrated knowledge base for the model Gram-positive bacterium Bacillus subtilis. This application allows a user to mine a variety of B. subtilis data sources, and analyse the resulting integrated dataset, which contains data about genes, gene products and their interactions. The data can be analysed either manually, by browsing using Ondex, or computationally via a Web services interface. We describe the process of creating a BacillOndex instance, and describe the use of the system for the analysis of single nucleotide polymorphisms in B. subtilis Marburg. The Marburg strain is the progenitor of the widely-used laboratory strain B. subtilis 168. We identified 27 SNPs with predictable phenotypic effects, including genetic traits for known phenotypes. We conclude that BacillOndex is a valuable tool for the systems-level investigation of, and hypothesis generation about, this important biotechnology workhorse. Such understanding contributes to our ability to construct synthetic genetic circuits in this organism.
    Journal of integrative bioinformatics 01/2013; 10(2):224.
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    ABSTRACT: Customers submit streams of jobs of different types for execution at a service center. The number of jobs in each stream and the rate of their submission are specified. A service level agreement indicates the charge paid by the customer, the quality of service promised by the provider and the penalty to be paid by the latter if the QoS requirement is not met. To save energy, servers may be powered up and down dynamically. The objective is to maximize the revenues received while minimizing the penalties paid and the energy consumption costs of the servers used. To that end, heuristic policies are proposed for making decisions about stream admissions and server activation and deactivation. Those policies are motivated by queueing models. The results of several simulation experiments are described.
    Electronic Notes in Theoretical Computer Science 01/2013; 296:199–210.
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    ABSTRACT: A constant influx of new data poses a challenge in keeping the annotation in biological databases current. Most biological databases contain significant quantities of textual annotation, which often contains the richest source of knowledge. Many databases reuse existing knowledge; during the curation process annotations are often propagated between entries. However, this is often not made explicit. Therefore, it can be hard, potentially impossible, for a reader to identify where an annotation originated from. Within this work we attempt to identify annotation provenance and track its subsequent propagation. Specifically, we exploit annotation reuse within the UniProt Knowledgebase (UniProtKB), at the level of individual sentences. We describe a visualisation approach for the provenance and propagation of sentences in UniProtKB which enables a large-scale statistical analysis. Initially levels of sentence reuse within UniProtKB were analysed, showing that reuse is heavily prevalent, which enables the tracking of provenance and propagation. By analysing sentences throughout UniProtKB, a number of interesting propagation patterns were identified, covering over [Formula: see text] sentences. Over [Formula: see text] sentences remain in the database after they have been removed from the entries where they originally occurred. Analysing a subset of these sentences suggest that approximately [Formula: see text] are erroneous, whilst [Formula: see text] appear to be inconsistent. These results suggest that being able to visualise sentence propagation and provenance can aid in the determination of the accuracy and quality of textual annotation. Source code and supplementary data are available from the authors website at http://homepages.cs.ncl.ac.uk/m.j.bell1/sentence_analysis/.
    PLoS ONE 01/2013; 8(10):e75541.
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    ABSTRACT: Mobile ad hoc networks are becoming very attractive and useful in many kinds of communication and networking applications. Due to the advantage of numerical analysis, analytical modelling formalisms, such as stochastic Petri nets, queuing networks and stochastic process algebra have been widely used for performance analysis of communication systems. To the best of our knowledge, there is no previous analytical study that analyses the performance of multi-hop ad hoc networks, where mobile nodes move according to a random mobility model in terms of the end-to-end delay and throughput. This work presents a novel analytical framework developed using stochastic reward nets for modelling and analysis of multi-hop ad hoc networks, based on the IEEE 802.11 DCF MAC protocol, where mobile nodes move according to the random waypoint mobility model. The proposed framework is used to analyse the performance of multi-hop ad hoc networks as a function of network parameters such as the transmission range, carrier sensing range, interference range, number of nodes, network area size, packet size, and packet generation rate. The proposed framework is organized into several models to break up the complexity of modelling the complete network, and make it easier to analyse each model as required. The framework is based on the idea of decomposition and fixed point iteration of stochastic reward nets. The proposed models are validated using extensive simulations.
    Simulation Modelling Practice and Theory 01/2013; 38:69–97.
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    ABSTRACT: The human connectome at the level of fiber tracts between brain regions has been shown to differ in patients with brain disorders compared to healthy control groups. Nonetheless, there is a potentially large number of different network organizations for individual patients that could lead to cognitive deficits prohibiting correct diagnosis. Therefore changes that can distinguish groups might not be sufficient to diagnose the disease that an individual patient suffers from and to indicate the best treatment option for that patient. We describe the challenges introduced by the large variability of connectomes within healthy subjects and patients and outline three common strategies to use connectomes as biomarkers of brain diseases. Finally, we propose a fourth option in using models of simulated brain activity (the dynamic connectome) based on structural connectivity rather than the structure (connectome) itself as a biomarker of disease. Dynamic connectomes, in addition to currently used structural, functional, or effective connectivity, could be an important future biomarker for clinical applications.
    Frontiers in Human Neuroscience 01/2013; 7:484.
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    ABSTRACT: In service-oriented systems, fault detection and localisation are not straightforward, and client-side fault-tolerance techniques are required to reduce the impact of faults on the quality of service experienced by the user. Restart is a well-known client-side technique for improving performance and service availability. With restart, tasks whose completion-time exceeds a timeout are re-issued by the client, with the goal of obtaining a shorter completion-time on the next attempt. Evaluation of restart should be performed by a combination of analysis, simulation, and measurement. In this paper we present the SFERA framework for simulation of restart in complex SOA systems. We illustrate SFERA features with an evaluation of the optimal restart timeout in a complex SOA system. We simulate a SOA system using different scenarios and model component response-times by phase-type distributions fitted to measurements from a SOA testbed. We observe and compare completion times for different scenarios.
    Electronic Notes in Theoretical Computer Science 01/2013; 291:3–14.
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