TY  - JOUR
T1  - Precise montaging and metric quantification of retinal surface area from ultra-widefield fundus photography and fluorescein angiography
JF  - Ophthalmic Surg Lasers Imaging Retina
Y1  - 2014
A1  - Croft, D.E.
A1  - van Hemert, J.
A1  - Wykoff, C.C.
A1  - Clifton, D.
A1  - Verhoek, M.
A1  - Fleming, A.
A1  - Brown, D.M.
KW  - medical
KW  - retinal imaging
AB  - BACKGROUND AND OBJECTIVE: Accurate quantification of retinal surface area from ultra-widefield (UWF) images is challenging due to warping produced when the retina is projected onto a two-dimensional plane for analysis. By accounting for this, the authors sought to precisely montage and accurately quantify retinal surface area in square millimeters. PATIENTS AND METHODS: Montages were created using Optos 200Tx (Optos, Dunfermline, U.K.) images taken at different gaze angles. A transformation projected the images to their correct location on a three-dimensional model. Area was quantified with spherical trigonometry. Warping, precision, and accuracy were assessed. RESULTS: Uncorrected, posterior pixels represented up to 79% greater surface area than peripheral pixels. Assessing precision, a standard region was quantified across 10 montages of the same eye (RSD: 0.7%; mean: 408.97 mm(2); range: 405.34-413.87 mm(2)). Assessing accuracy, 50 patients' disc areas were quantified (mean: 2.21 mm(2); SE: 0.06 mm(2)), and the results fell within the normative range. CONCLUSION: By accounting for warping inherent in UWF images, precise montaging and accurate quantification of retinal surface area in square millimeters were achieved. [Ophthalmic Surg Lasers Imaging Retina. 2014;45:312-317.].
VL  - 45
ER  - 

TY  - JOUR
T1  - Quantification of Ultra-Widefield Retinal Images
JF  - Retina Today
Y1  - 2014
A1  - D.E. Croft
A1  - C.C. Wykoff
A1  - D.M. Brown
A1  - van Hemert, J.
A1  - M. Verhoek
KW  - medical
KW  - retinal imaging
AB  - Advances in imaging periodically lead to dramatic changes in the diagnosis, management, and study of retinal disease. For example, the innovation and wide-spread application of fluorescein angiography and optical coherence tomography (OCT) have had tremendous impact on the management of retinal disorders.1,2 Recently, ultra-widefield (UWF) imaging has opened a new window into the retina, allowing the capture of greater than 80% of the fundus with a single shot.3 With montaging, much of the remaining retinal surface area can be captured.4,5 However, to maximize the potential of these new modalities, accurate quantification of the pathology they capture is critical.
UR  - http://www.bmctoday.net/retinatoday/pdfs/0514RT_imaging_Croft.pdf
ER  - 

TY  - BOOK
T1  - The DATA Bonanza: Improving Knowledge Discovery in Science, Engineering, and Business
T2  - Wiley Series on Parallel and Distributed Computing (Editor: Albert Y. Zomaya)
Y1  - 2013
A1  - Atkinson, Malcolm P.
A1  - Baxter, Robert M.
A1  - Peter Brezany
A1  - Oscar Corcho
A1  - Michelle Galea
A1  - Parsons, Mark
A1  - Snelling, David
A1  - van Hemert, Jano
KW  - Big Data
KW  - Data Intensive
KW  - data mining
KW  - Data Streaming
KW  - Databases
KW  - Dispel
KW  - Distributed Computing
KW  - Knowledge Discovery
KW  - Workflows
AB  - With the digital revolution opening up tremendous opportunities in many fields, there is a growing need for skilled professionals who can develop data-intensive systems and extract information and knowledge from them. This book frames for the first time a new systematic approach for tackling the challenges of data-intensive computing, providing decision makers and technical experts alike with practical tools for dealing with our exploding data collections.  Emphasising data-intensive thinking and interdisciplinary collaboration,  The DATA Bonanza: Improving Knowledge Discovery in Science, Engineering, and Business examines the essential components of knowledge discovery, surveys many of the current research efforts worldwide, and points to new areas for innovation. Complete with a wealth of examples and DISPEL-based methods demonstrating how to gain more from data in real-world systems, the book:  * Outlines the concepts and rationale for implementing data-intensive computing in organisations  * Covers from the ground up problem-solving strategies for data analysis in a data-rich world  * Introduces techniques for data-intensive engineering using the Data-Intensive Systems Process Engineering Language DISPEL  * Features in-depth case studies in customer relations, environmental hazards, seismology, and more  * Showcases successful applications in areas ranging from astronomy and the humanities to transport engineering  * Includes sample program snippets throughout the text as well as additional materials on a companion website  The DATA Bonanza is a must-have guide for information strategists, data analysts, and engineers in business, research, and government, and for anyone wishing to be on the cutting edge of data mining, machine learning, databases, distributed systems, or large-scale computing.
JF  - Wiley Series on Parallel and Distributed Computing (Editor: Albert Y. Zomaya)
PB  - John Wiley & Sons Inc.
SN  - 978-1-118-39864-7
ER  - 

TY  - CHAP
T1  - Data-Intensive Analysis
T2  - THE DATA BONANZA: Improving Knowledge Discovery for Science, Engineering and Business
Y1  - 2013
A1  - Oscar Corcho
A1  - van Hemert, Jano
ED  - Malcolm Atkinson
ED  - Rob Baxter
ED  - Peter Brezany
ED  - Oscar Corcho
ED  - Michelle Galea
ED  - Parsons, Mark
ED  - Snelling, David
ED  - van Hemert, Jano
KW  - data mining
KW  - Data-Analysis Experts
KW  - Data-Intensive Analysis
KW  - Knowledge Discovery
AB  - Part II: "Data-intensive Knowledge Discovery", focuses on the needs of data-analysis experts. It illustrates the problem-solving strategies appropriate for a data-rich world, without delving into the details of underlying technologies. It should engage and inform data-analysis specialists, such as statisticians, data miners, image analysts, bio-informaticians or chemo-informaticians, and generate  ideas pertinent to their application areas.    Chapter 5: "Data-intensive Analysis", introduces a set of common problems that data-analysis experts often encounter, by means of a set of scenarios of increasing levels of complexity. The scenarios typify knowledge discovery challenges and the presented solutions provide practical methods; a starting point for readers addressing their own data challenges.
JF  - THE DATA BONANZA: Improving Knowledge Discovery for Science, Engineering and Business
PB  - John Wiley & Sons Ltd.
ER  - 

TY  - CHAP
T1  - Data-Intensive Components and Usage Patterns
T2  - THE DATA BONANZA: Improving Knowledge Discovery for Science, Engineering and Business
Y1  - 2013
A1  - Oscar Corcho
ED  - Malcolm Atkinson
ED  - Rob Baxter
ED  - Peter Brezany
ED  - Oscar Corcho
ED  - Michelle Galea
ED  - Parsons, Mark
ED  - Snelling, David
ED  - van Hemert, Jano
KW  - Data Analysis
KW  - data mining
KW  - Data-Intensive Components
KW  - Registry
KW  - Workflow Libraries
KW  - Workflow Sharing
AB  - Chapter 7: "Data-intensive components and usage patterns", provides a systematic review of the components that are commonly used in knowledge discovery tasks as well as common patterns of component composition. That is, it introduces the processing elements from which knowledge discovery solutions are built and common composition patterns for delivering trustworthy information.  It reflects on how these components and patterns are evolving in a data-intensive context.
JF  - THE DATA BONANZA: Improving Knowledge Discovery for Science, Engineering and Business
PB  - John Wiley & Sons Ltd.
ER  - 

TY  - CHAP
T1  - The Data-Intensive Survival Guide
T2  - THE DATA BONANZA: Improving Knowledge Discovery for Science, Engineering and Business
Y1  - 2013
A1  - Malcolm Atkinson
ED  - Malcolm Atkinson
ED  - Rob Baxter
ED  - Peter Brezany
ED  - Oscar Corcho
ED  - Michelle Galea
ED  - Parsons, Mark
ED  - Snelling, David
ED  - van Hemert, Jano
KW  - Data-Analysis Experts
KW  - Data-Intensive Architecture
KW  - Data-intensive Computing
KW  - Data-Intensive Engineers
KW  - Datascopes
KW  - Dispel
KW  - Domain Experts
KW  - Intellectual Ramps
KW  - Knowledge Discovery
KW  - Workflows
AB  - Chapter 3: "The data-intensive survival guide", presents an overview of all of the elements of the proposed data-intensive strategy. Sufficient detail is presented for readers to understand the principles and practice that we recommend. It should also provide a good preparation for readers who choose to sample later chapters. It introduces three professional viewpoints: domain experts, data-analysis experts, and data-intensive engineers. Success depends on a balanced approach that develops the capacity of all three groups. A data-intensive architecture provides a flexible framework for that balanced approach. This enables the three groups to build and exploit data-intensive processes that incrementally step from data to results. A language is introduced to describe these incremental data processes from all three points of view. The chapter introduces ‘datascopes’ as the productized data-handling environments and ‘intellectual ramps’ as the ‘on ramps’  for the highways from data to knowledge.
JF  - THE DATA BONANZA: Improving Knowledge Discovery for Science, Engineering and Business
PB  - John Wiley & Sons Ltd.
ER  - 

TY  - CHAP
T1  - Data-Intensive Thinking with DISPEL
T2  - THE DATA BONANZA: Improving Knowledge Discovery for Science, Engineering and Business
Y1  - 2013
A1  - Malcolm Atkinson
ED  - Malcolm Atkinson
ED  - Rob Baxter
ED  - Peter Brezany
ED  - Oscar Corcho
ED  - Michelle Galea
ED  - Parsons, Mark
ED  - Snelling, David
ED  - van Hemert, Jano
KW  - Data-Intensive Machines
KW  - Data-Intensive Thinking, Data-intensive Computing
KW  - Dispel
KW  - Distributed Computing
KW  - Knowledge Discovery
AB  - Chapter 4: "Data-intensive thinking with DISPEL", engages the reader with technical issues and solutions, by working through a sequence of examples, building up from a sketch of a solution to a large-scale data challenge. It uses the DISPEL language extensively, introducing its concepts and constructs. It shows how DISPEL may help designers, data-analysts, and engineers develop  solutions to the requirements emerging in any data-intensive application domain. The reader is taken through simple steps initially, this then builds to conceptually complex steps that are necessary to cope with the realities of real data providers, real data, real distributed systems, and long-running processes.
JF  - THE DATA BONANZA: Improving Knowledge Discovery for Science, Engineering and Business
PB  - John Wiley & Sons Inc.
ER  - 

TY  - CHAP
T1  - Definition of the DISPEL Language
T2  - THE DATA BONANZA: Improving Knowledge Discovery for Science, Engineering and Business
Y1  - 2013
A1  - Paul Martin
A1  - Yaikhom, Gagarine
ED  - Malcolm Atkinson
ED  - Rob Baxter
ED  - Peter Brezany
ED  - Oscar Corcho
ED  - Michelle Galea
ED  - Parsons, Mark
ED  - Snelling, David
ED  - van Hemert, Jano
KW  - Data Streaming
KW  - Data-intensive Computing
KW  - Dispel
AB  - Chapter 10: "Definition of the DISPEL language", describes the novel aspects of the DISPEL language: its constructs, capabilities, and anticipated programming style.
JF  - THE DATA BONANZA: Improving Knowledge Discovery for Science, Engineering and Business
T3  - {Parallel and Distributed Computing, series editor Albert Y. Zomaya}
PB  - John Wiley & Sons Inc.
ER  - 

TY  - CHAP
T1  - The Digital-Data Challenge
T2  - THE DATA BONANZA: Improving Knowledge Discovery for Science, Engineering and Business
Y1  - 2013
A1  - Malcolm Atkinson
A1  - Parsons, Mark
ED  - Malcolm Atkinson
ED  - Rob Baxter
ED  - Peter Brezany
ED  - Oscar Corcho
ED  - Michelle Galea
ED  - Parsons, Mark
ED  - Snelling, David
ED  - van Hemert, Jano
KW  - Big Data
KW  - Data-intensive Computing, Knowledge Discovery
KW  - Digital Data
KW  - Digital-Data Revolution
AB  - Part I: <em>Strategies for success in the digital-data revolution</em>, provides an executive summary of the whole book to convince strategists, politicians, managers, and educators that our future data-intensive society requires new thinking, new behavior, new culture, and new distribution of investment and effort. This part will introduce the major concepts so that readers are equipped to discuss and steer their organization’s response to the opportunities and obligations brought by the growing wealth of data. It will help readers understand the changing context brought about by advances in digital devices, digital communication, and ubiquitous computing.    Chapter 1: <em>The digital-data challenge</em>, will help readers to understand the challenges ahead in making good use of the data and introduce ideas that will lead to helpful strategies. A global digital-data revolution is catalyzing change in the ways in which we live, work, relax, govern, and organize. This is a significant change in society, as important as the invention of printing or the industrial revolution, but more challenging because it is happening globally at lnternet speed. Becoming agile in adapting to this new world is essential.
JF  - THE DATA BONANZA: Improving Knowledge Discovery for Science, Engineering and Business
PB  - John Wiley & Sons Ltd.
ER  - 

TY  - CHAP
T1  - The Digital-Data Revolution
T2  - THE DATA BONANZA: Improving Knowledge Discovery for Science, Engineering and Business
Y1  - 2013
A1  - Malcolm Atkinson
ED  - Malcolm Atkinson
ED  - Rob Baxter
ED  - Peter Brezany
ED  - Oscar Corcho
ED  - Michelle Galea
ED  - Parsons, Mark
ED  - Snelling, David
ED  - van Hemert, Jano
KW  - Data
KW  - Information
KW  - Knowledge
KW  - Knowledge Discovery
KW  - Social Impact of Digital Data
KW  - Wisdom, Data-intensive Computing
AB  - Chapter 2: "The digital-data revolution", reviews the relationships between data, information, knowledge, and wisdom. It analyses and quantifies the changes in technology and society that are delivering the data bonanza, and then reviews the consequential changes via representative examples in biology, Earth sciences, social sciences, leisure activity, and business. It exposes quantitative details and shows the complexity and diversity of the growing wealth of data, introducing some of its potential benefits and examples of the impediments to successfully realizing those benefits.
JF  - THE DATA BONANZA: Improving Knowledge Discovery for Science, Engineering and Business
PB  - John Wiley & Sons Ltd.
ER  - 

TY  - CHAP
T1  - DISPEL Development
T2  - THE DATA BONANZA: Improving Knowledge Discovery for Science, Engineering and Business
Y1  - 2013
A1  - Adrian Mouat
A1  - Snelling, David
ED  - Malcolm Atkinson
ED  - Rob Baxter
ED  - Peter Brezany
ED  - Oscar Corcho
ED  - Michelle Galea
ED  - Parsons, Mark
ED  - Snelling, David
ED  - van Hemert, Jano
KW  - Diagnostics
KW  - Dispel
KW  - IDE
KW  - Libraries
KW  - Processing Elements
AB  - Chapter 11: "DISPEL development", describes the tools and libraries that a DISPEL developer might expect to use. The tools include those needed during process definition, those required to organize enactment, and diagnostic aids for developers of applications and platforms.
JF  - THE DATA BONANZA: Improving Knowledge Discovery for Science, Engineering and Business
PB  - John Wiley & Sons Inc.
ER  - 

TY  - CHAP
T1  - DISPEL Enactment
T2  - THE DATA BONANZA: Improving Knowledge Discovery for Science, Engineering and Business
Y1  - 2013
A1  - Chee Sun Liew
A1  - Krause, Amrey
A1  - Snelling, David
ED  - Malcolm Atkinson
ED  - Rob Baxter
ED  - Peter Brezany
ED  - Oscar Corcho
ED  - Michelle Galea
ED  - Parsons, Mark
ED  - Snelling, David
ED  - van Hemert, Jano
KW  - Data Streaming
KW  - Data-Intensive Engineering
KW  - Dispel
KW  - Workflow Enactment
AB  - Chapter 12: "DISPEL enactment", describes the four stages of DISPEL enactment. It is targeted at the data-intensive engineers who implement enactment services.
JF  - THE DATA BONANZA: Improving Knowledge Discovery for Science, Engineering and Business
PB  - John Wiley & Sons Inc.
ER  - 

TY  - CHAP
T1  - Foreword
T2  - THE DATA BONANZA: Improving Knowledge Discovery for Science, Engineering and Business
Y1  - 2013
A1  - Tony Hey
ED  - Malcolm Atkinson
ED  - Rob Baxter
ED  - Peter Brezany
ED  - Oscar Corcho
ED  - Michelle Galea
ED  - Parsons, Mark
ED  - Snelling, David
ED  - van Hemert, Jano
KW  - Big Data
KW  - Data-intensive Computing, Knowledge Discovery
JF  - THE DATA BONANZA: Improving Knowledge Discovery for Science, Engineering and Business
PB  - John Wiley & Sons Ltd.
ER  - 

TY  - JOUR
T1  - Lesion Area Detection Using Source Image Correlation Coefficient for CT Perfusion Imaging
JF  - IEEE Journal of Biomedical and Health Informatics
Y1  - 2013
A1  - Fan Zhu
A1  - Rodríguez, David
A1  - Carpenter, Trevor K.
A1  - Atkinson, Malcolm P.
A1  - Wardlaw, Joanna M.
KW  - CT , Pattern Recognition , Perfusion Source Images , Segmentation
AB  - Computer tomography (CT) perfusion imaging is widely used to calculate brain hemodynamic quantities such as Cerebral Blood Flow (CBF), Cerebral Blood Volume (CBV) and Mean Transit Time (MTT) that aid the diagnosis of acute stroke. Since perfusion source images contain more information than hemodynamic maps, good utilisation of the source images can lead to better understanding than the hemodynamic maps alone. Correlation-coefficient tests are used in our approach to measure the similarity between healthy tissue time-concentration curves and unknown curves. This information is then used to differentiate penumbra and dead tissues from healthy tissues. The goal of the segmentation is to fully utilize information in the perfusion source images. Our method directly identifies suspected abnormal areas from perfusion source images and then delivers a suggested segmentation of healthy, penumbra and dead tissue. This approach is designed to handle CT perfusion images, but it can also be used to detect lesion areas in MR perfusion images.
VL  - 17
IS  - 5
ER  - 

TY  - CHAP
T1  - Platforms for Data-Intensive Analysis
T2  - THE DATA BONANZA: Improving Knowledge Discovery for Science, Engineering and Business
Y1  - 2013
A1  - Snelling, David
ED  - Malcolm Atkinson
ED  - Baxter, Robert M.
ED  - Peter Brezany
ED  - Oscar Corcho
ED  - Michelle Galea
ED  - Parsons, Mark
ED  - Snelling, David
ED  - van Hemert, Jano
KW  - Data-Intensive Engineering
KW  - Data-Intensive Systems
KW  - Dispel
KW  - Distributed Systems
AB  - Part III: "Data-intensive engineering", is targeted at technical experts who will develop complex applications, new components, or data-intensive platforms.  The techniques introduced may be applied very widely; for example, to any data-intensive distributed application, such as index generation, image processing, sequence comparison, text analysis, and sensor-stream monitoring. The challenges, methods, and implementation requirements are illustrated by making extensive use of DISPEL.    Chapter 9: "Platforms for data-intensive analysis", gives a reprise of data-intensive architectures, examines the business case for investing in them, and introduces the stages of data-intensive workflow enactment.
JF  - THE DATA BONANZA: Improving Knowledge Discovery for Science, Engineering and Business
PB  - John Wiley & Sons Ltd.
ER  - 

TY  - CHAP
T1  - Preface
T2  - THE DATA BONANZA: Improving Knowledge Discovery for Science, Engineering and Business
Y1  - 2013
A1  - Malcolm Atkinson
ED  - Malcolm Atkinson
ED  - Rob Baxter
ED  - Peter Brezany
ED  - Oscar Corcho
ED  - Michelle Galea
ED  - Parsons, Mark
ED  - Snelling, David
ED  - van Hemert, Jano
KW  - Big Data, Data-intensive Computing, Knowledge Discovery
AB  - Who should read the book and why.  The structure and conventions used.  Suggested reading paths for different categories of reader.
JF  - THE DATA BONANZA: Improving Knowledge Discovery for Science, Engineering and Business
PB  - John Wiley & Sons Ltd.
ER  - 

TY  - CHAP
T1  - Problem Solving in Data-Intensive Knowledge Discovery
T2  - THE DATA BONANZA: Improving Knowledge Discovery for Science, Engineering and Business
Y1  - 2013
A1  - Oscar Corcho
A1  - van Hemert, Jano
ED  - Malcolm Atkinson
ED  - Rob Baxter
ED  - Peter Brezany
ED  - Oscar Corcho
ED  - Michelle Galea
ED  - Parsons, Mark
ED  - Snelling, David
ED  - van Hemert, Jano
KW  - Data-Analysis Experts
KW  - Data-Intensive Analysis
KW  - Design Patterns for Knowledge Discovery
KW  - Knowledge Discovery
AB  - Chapter 6: "Problem solving in data-intensive knowledge discovery", on the basis of the previous scenarios, this chapter provides an overview of effective strategies in knowledge discovery, highlighting common problem-solving methods that apply in conventional contexts, and focusing on the similarities and differences of these methods.
JF  - THE DATA BONANZA: Improving Knowledge Discovery for Science, Engineering and Business
PB  - John Wiley & Sons Ltd.
ER  - 

TY  - CONF
T1  - Provenance for seismological processing pipelines in a distributed streaming workflow
T2  - EDBT/ICDT Workshops
Y1  - 2013
A1  - Alessandro Spinuso
A1  - James Cheney
A1  - Malcolm Atkinson
JF  - EDBT/ICDT Workshops
ER  - 

TY  - CHAP
T1  - Sharing and Reuse in Knowledge Discovery
T2  - THE DATA BONANZA: Improving Knowledge Discovery for Science, Engineering and Business
Y1  - 2013
A1  - Oscar Corcho
ED  - Malcolm Atkinson
ED  - Rob Baxter
ED  - Peter Brezany
ED  - Oscar Corcho
ED  - Michelle Galea
ED  - Parsons, Mark
ED  - Snelling, David
ED  - van Hemert, Jano
KW  - Data-Intensive Analysis
KW  - Knowledge Discovery
KW  - Ontologies
KW  - Semantic Web
KW  - Sharing
AB  - Chapter 8: "Sharing and re-use in knowledge discovery", introduces more advanced knowledge discovery problems, and shows how improved component and pattern descriptions facilitate re-use. This supports the assembly of libraries of high level components well-adapted to classes of knowledge discovery methods or application domains. The descriptions are made more powerful by introducing notations from the semantic Web.
JF  - THE DATA BONANZA: Improving Knowledge Discovery for Science, Engineering and Business
PB  - John Wiley & Sons Ltd.
ER  - 

TY  - CONF
T1  - Towards Addressing CPU-Intensive Seismological Applications in Europe
T2  - International Supercomputing Conference
Y1  - 2013
A1  - Michele Carpené
A1  - I.A. Klampanos
A1  - Siew Hoon Leong
A1  - Emanuele Casarotti
A1  - Peter Danecek
A1  - Graziella Ferini
A1  - Andre Gemünd
A1  - Amrey Krause
A1  - Lion Krischer
A1  - Federica Magnoni
A1  - Marek Simon
A1  - Alessandro Spinuso
A1  - Luca Trani
A1  - Malcolm Atkinson
A1  - Giovanni Erbacci
A1  - Anton Frank
A1  - Heiner Igel
A1  - Andreas Rietbrock
A1  - Horst Schwichtenberg
A1  - Jean-Pierre Vilotte
AB  - Advanced application environments for seismic analysis help geoscientists to execute complex simulations to predict the behaviour of a geophysical system and potential surface observations. At the same time data collected from seismic stations must be processed comparing recorded signals with predictions. The EU-funded project VERCE (http://verce.eu/) aims to enable specific seismological use-cases and, on the basis of requirements elicited from the seismology community, provide a service-oriented infrastructure to deal with such challenges. In this paper we present VERCE’s architecture, in particular relating to forward and inverse modelling of Earth models and how the, largely file-based, HPC model can be combined with data streaming operations to enhance the scalability of experiments.We posit that the integration of services and HPC resources in an open, collaborative environment is an essential medium for the advancement of sciences of critical importance, such as seismology.
JF  - International Supercomputing Conference
CY  - Leipzig, Germany
ER  - 

TY  - CONF
T1  - The W3C PROV family of specifications for modelling provenance metadata
T2  - EDBT
Y1  - 2013
A1  - Paolo Missier
A1  - Khalid Belhajjame
A1  - James Cheney
JF  - EDBT
ER  - 

TY  - JOUR
T1  - Computed Tomography Perfusion Imaging Denoising Using Gaussian Process Regression
JF  - Physics in Medicine and Biology
Y1  - 2012
A1  - Fan Zhu
A1  - Carpenter, Trevor
A1  - Rodríguez, David
A1  - Malcolm Atkinson
A1  - Wardlaw, Joanna
AB  - Objective: Brain perfusion weighted images acquired using dynamic contrast studies have an important clinical role in acute stroke diagnosis and treatment decisions. However, Computed Tomography (CT) images suffer from low contrast-to-noise ratios (CNR) as a consequence of the limitation of the exposure to radiation of the patient. As a consequence, the developments of methods for improving the CNR are valuable. Methods: The majority of existing approaches for denoising CT images are optimized for 3D (spatial) information, including spatial decimation (spatially weighted mean filters) and techniques based on wavelet and curvelet transforms. However, perfusion imaging data is 4D as it also contains temporal information. Our approach using Gaussian process regression (GPR), which takes advantage of the temporal information, to reduce the noise level. Results: Over the entire image, GPR gains a 99% CNR improvement over the raw images and also improves the quality of haemodynamic maps allowing a better identification of edges and detailed information. At the level of individual voxel, GPR provides a stable baseline, helps us to identify key parameters from tissue time- concentration curves and reduces the oscillations in the curve. Conclusion: GPR is superior to the comparable techniques used in this study.
ER  - 

TY  - JOUR
T1  - Consistency and repair for XML write-access control policies
JF  - VLDB J.
Y1  - 2012
A1  - Loreto Bravo
A1  - James Cheney
A1  - Irini Fundulaki
A1  - Ricardo Segovia
VL  - 21
ER  - 

TY  - CONF
T1  - A Core Calculus for Provenance
T2  - POST
Y1  - 2012
A1  - Umut A. Acar
A1  - Amal Ahmed
A1  - James Cheney
A1  - Roly Perera
JF  - POST
ER  - 

TY  - JOUR
T1  - Data-Intensive Architecture for Scientific Knowledge Discovery
JF  - Distributed and Parallel Databases
Y1  - 2012
A1  - Atkinson, Malcolm P.
A1  - Chee Sun Liew
A1  - Michelle Galea
A1  - Paul Martin
A1  - Krause, Amrey
A1  - Adrian Mouat
A1  - Oscar Corcho
A1  - Snelling, David
KW  - Knowledge discovery, workflow management system
AB  - This paper presents a data-intensive architecture that demonstrates the ability to support applications from a wide range of application domains, and support the different types of users involved in defining, designing and executing data-intensive processing tasks. The prototype architecture is introduced, and the pivotal role of DISPEL as a canonical language is explained. The architecture promotes the exploration and exploitation of distributed and heterogeneous data and spans the complete knowledge discovery process, from data preparation, to analysis, to evaluation and reiteration. The architecture evaluation included large-scale applications from astronomy, cosmology, hydrology, functional genetics, imaging processing and seismology.
VL  - 30
UR  - http://dx.doi.org/10.1007/s10619-012-7105-3
IS  - 5
ER  - 

TY  - JOUR
T1  - Dimensioning Scientific Computing Systems to Improve Performance of Map-Reduce based Applications
JF  - Procedia CS
Y1  - 2012
A1  - Gabriel G. Castañè
A1  - Alberto Nuñez
A1  - Rosa Filgueira
A1  - Jesus Carretero
VL  - 9
ER  - 

TY  - CONF
T1  - Dimensioning Scientific Computing Systems to Improve Performance of Map-Reduce based Applications
T2  - Procedia Computer Science, Proceedings of the International Conference on Computational Science, ICCS 2012
Y1  - 2012
A1  - Gabriel G. Castañè
A1  - Alberto Nuñez
A1  - Rosa Filgueira
A1  - Jesus Carretero
JF  - Procedia Computer Science, Proceedings of the International Conference on Computational Science, ICCS 2012
ER  - 

TY  - JOUR
T1  - Parallel perfusion imaging processing using GPGPU
JF  - Computer Methods and Programs in Biomedicine
Y1  - 2012
A1  - Fan Zhu
A1  - Rodríguez, David
A1  - Carpenter, Trevor
A1  - Malcolm Atkinson
A1  - Wardlaw, Joanna
KW  - Deconvolution
KW  - GPGPU
KW  - Local AIF
KW  - Parallelization
KW  - Perfusion Imaging
AB  - Background and purpose The objective of brain perfusion quantification is to generate parametric maps of relevant hemodynamic quantities such as cerebral blood flow (CBF), cerebral blood volume (CBV) and mean transit time (MTT) that can be used in diagnosis of acute stroke. These calculations involve deconvolution operations that can be very computationally expensive when using local Arterial Input Functions (AIF). As time is vitally important in the case of acute stroke, reducing the analysis time will reduce the number of brain cells damaged and increase the potential for recovery. Methods GPUs originated as graphics generation dedicated co-processors, but modern GPUs have evolved to become a more general processor capable of executing scientific computations. It provides a highly parallel computing environment due to its large number of computing cores and constitutes an affordable high performance computing method. In this paper, we will present the implementation of a deconvolution algorithm for brain perfusion quantification on GPGPU (General Purpose Graphics Processor Units) using the CUDA programming model. We present the serial and parallel implementations of such algorithms and the evaluation of the performance gains using GPUs. Results Our method has gained a 5.56 and 3.75 speedup for CT and MR images respectively. Conclusions It seems that using GPGPU is a desirable approach in perfusion imaging analysis, which does not harm the quality of cerebral hemodynamic maps but delivers results faster than the traditional computation.
UR  - http://www.sciencedirect.com/science/article/pii/S0169260712001587
ER  - 

TY  - JOUR
T1  - Principles of Provenance (Dagstuhl Seminar 12091)
JF  - Dagstuhl Reports
Y1  - 2012
A1  - James Cheney
A1  - Anthony Finkelstein
A1  - Bertram Ludäscher
A1  - Stijn Vansummeren
VL  - 2
ER  - 

TY  - JOUR
T1  - Requirements for Provenance on the Web
JF  - IJDC
Y1  - 2012
A1  - Paul T. Groth
A1  - Yolanda Gil
A1  - James Cheney
A1  - Simon Miles
VL  - 7
ER  - 

TY  - JOUR
T1  - SIMCAN: A flexible, scalable and expandable simulation platform for modelling and simulating distributed architectures and applications
JF  - Simulation Modelling Practice and Theory
Y1  - 2012
A1  - Alberto Nuñez
A1  - Javier Fernández
A1  - Rosa Filgueira
A1  - Félix García Carballeira
A1  - Jesús Carretero
VL  - 20
ER  - 

TY  - CONF
T1  - The Use of Reputation as Noise-resistant Selection Bias in a Co-evolutionary Multi-agent System
T2  - Genetic and Evolutionary Computation Conference
Y1  - 2012
A1  - Nikolaos Chatzinikolaou
A1  - Dave Robertson
JF  - Genetic and Evolutionary Computation Conference
CY  - Philadelphia
ER  - 

TY  - RPRT
T1  - EDIM1 Progress Report
Y1  - 2011
A1  - Paul Martin
A1  - Malcolm Atkinson
A1  - Parsons, Mark
A1  - Adam Carter
A1  - Gareth Francis
AB  - The Edinburgh Data-Intensive Machine (EDIM1) is the product of a joint collaboration between the data-intensive group at the School of Informatics and EPCC. EDIM1 is an experimental system, offering an alternative architecture for data-intensive computation and providing a platform for evaluating tools for data-intensive research; a 120 node cluster of ‘data-bricks’ with high storage yet modest computational capacity. This document gives some background into the context in which EDIM1 was designed and constructed, as well as providing an overview of its use so far and future plans.
ER  - 

TY  - JOUR
T1  - Managing dynamic enterprise and urgent workloads on clouds using layered queuing and historical performance models
JF  - Simulation Modelling Practice and Theory
Y1  - 2011
A1  - David A. Bacigalupo
A1  - van Hemert, Jano I.
A1  - Xiaoyu Chen
A1  - Asif Usmani
A1  - Adam P. Chester
A1  - Ligang He
A1  - Donna N. Dillenberger
A1  - Gary B. Wills
A1  - Lester Gilbert
A1  - Stephen A. Jarvis
KW  - e-Science
AB  - The automatic allocation of enterprise workload to resources can be enhanced by being able to make what–if response time predictions whilst different allocations are being considered. We experimentally investigate an historical and a layered queuing performance model and show how they can provide a good level of support for a dynamic-urgent cloud environment. Using this we define, implement and experimentally investigate the effectiveness of a prediction-based cloud workload and resource management algorithm. Based on these experimental analyses we: (i) comparatively evaluate the layered queuing and historical techniques; (ii) evaluate the effectiveness of the management algorithm in different operating scenarios; and (iii) provide guidance on using prediction-based workload and resource management.
VL  - 19
ER  - 

TY  - CONF
T1  - A Parallel Deconvolution Algorithm in Perfusion Imaging
T2  - Healthcare Informatics, Imaging, and Systems Biology (HISB)
Y1  - 2011
A1  - Zhu, Fan.
A1  - Rodríguez, David
A1  - Carpenter, Trevor
A1  - Malcolm Atkinson
A1  - Wardlaw, Joanna
KW  - Deconvolution
KW  - GPGPU
KW  - Parallelization
KW  - Perfusion Imaging
AB  - In this paper, we will present the implementation of a deconvolution algorithm for brain perfusion quantification on GPGPU (General Purpose Graphics Processor Units) using the CUDA programming model. GPUs originated as graphics generation dedicated co-processors, but the modern GPUs have evolved to become a more general processor capable of executing scientific computations. It provides a highly parallel computing environment due to its huge number of computing cores and constitutes an affordable high performance computing method. The objective of brain perfusion quantification is to generate parametric maps of relevant haemodynamic quantities such as Cerebral Blood Flow (CBF), Cerebral Blood Volume (CBV) and Mean Transit Time (MTT) that can be used in diagnosis of conditions such as stroke or brain tumors. These calculations involve deconvolution operations that in the case of using local Arterial Input Functions (AIF) can be very expensive computationally. We present the serial and parallel implementations of such algorithm and the evaluation of the performance gains using GPUs.
JF  - Healthcare Informatics, Imaging, and Systems Biology (HISB)
CY  - San Jose, California
SN  - 978-1-4577-0325-6
UR  - http://ieeexplore.ieee.org/xpls/abs_all.jsp?arnumber=6061411&tag=1
ER  - 

TY  - JOUR
T1  - Performance database: capturing data for optimizing distributed streaming workflows
JF  - Philosophical Transactions of the Royal Society A: Mathematical, Physical and Engineering Sciences
Y1  - 2011
A1  - Chee Sun Liew
A1  - Atkinson, Malcolm P.
A1  - Radoslaw Ostrowski
A1  - Murray Cole
A1  - van Hemert, Jano I.
A1  - Liangxiu Han
KW  - measurement framework
KW  - performance data
KW  - streaming workflows
AB  - The performance database (PDB) stores performance-related data gathered during workflow enactment. We argue that by carefully understanding and manipulating this data, we can improve efficiency when enacting workflows. This paper describes the rationale behind the PDB, and proposes a systematic way to implement it. The prototype is built as part of the Advanced Data Mining and Integration Research for Europe project. We use workflows from real-world experiments to demonstrate the usage of PDB.
VL  - 369
IS  - 1949
ER  - 

TY  - CONF
T1  - RapidBrain: Developing a Portal for Brain Research Imaging
T2  - All Hands Meeting 2011, York
Y1  - 2011
A1  - Kenton D'Mellow
A1  - Rodríguez, David
A1  - Carpenter, Trevor
A1  - Jos Koetsier
A1  - Dominic Job
A1  - van Hemert, Jano
A1  - Wardlaw, Joanna
A1  - Fan Zhu
AB  - Brain imaging researchers execute complex multistep workflows in their computational analysis. Those workflows often include applications that have very different user interfaces and sometimes use different data formats. A good example is the brain perfusion quantification workflow used at the BRIC (Brain Research Imaging Centre) in Edinburgh.  Rapid provides an easy method for creating portlets for computational jobs, and at the same it is extensible.  We have exploited this extensibility with additions that stretch the functionality beyond the original limits. These changes can be used by other projects to create their own portals, but it should be noted that the development of such portals involve a greater effort than the required in the regular use of Rapid for creating portlets. In our case it has been used to provide a user-friendly interface for perfusion analysis that covers from volume
JF  - All Hands Meeting 2011, York
CY  - York
ER  - 

TY  - JOUR
T1  - A user-friendly web portal for T-Coffee on supercomputers
JF  - BMC Bioinformatics
Y1  - 2011
A1  - J. Rius
A1  - F. Cores
A1  - F. Solsona
A1  - van Hemert, J. I.
A1  - Koetsier, J.
A1  - C. Notredame
KW  - e-Science
KW  - portal
KW  - rapid
AB  - Background Parallel T-Coffee (PTC) was the first parallel implementation of the T-Coffee multiple sequence alignment tool. It is based on MPI and RMA mechanisms. Its purpose is to reduce the execution time of the large-scale sequence alignments. It can be run on distributed memory clusters allowing users to align data sets consisting of hundreds of proteins within a reasonable time. However, most of the potential users of this tool are not familiar with the use of grids or supercomputers. Results In this paper we show how PTC can be easily deployed and controlled on a super computer architecture using a web portal developed using Rapid. Rapid is a tool for efficiently generating standardized portlets for a wide range of applications and the approach described here is generic enough to be applied to other applications, or to deploy PTC on different HPC environments. Conclusions The PTC portal allows users to upload a large number of sequences to be aligned by the parallel version of TC that cannot be aligned by a single machine due to memory and execution time constraints. The web portal provides a user-friendly solution.
VL  - 12
UR  - http://www.biomedcentral.com/1471-2105/12/150
ER  - 

TY  - JOUR
T1  - Validation and mismatch repair of workflows through typed data streams
JF  - Philosophical Transactions of the Royal Society A: Mathematical, Physical and Engineering Sciences
Y1  - 2011
A1  - Yaikhom, Gagarine
A1  - Malcolm Atkinson
A1  - van Hemert, Jano
A1  - Oscar Corcho
A1  - Krause, Amy
AB  - The type system of a language guarantees that all of the operations on a set of data comply with the rules and conditions set by the language. While language typing is a fundamental requirement for any programming language, the typing of data that flow between processing elements within a workflow is currently being treated as optional. In this paper, we introduce a three-level type system for typing workflow data streams. These types are parts of the Data Intensive System Process Engineering Language programming language, which empowers users with the ability to validate the connections inside a workflow composition, and apply appropriate data type conversions when necessary. Furthermore, this system enables the enactment engine in carrying out type-directed workflow optimizations.
VL  - 369
IS  - 1949
ER  - 

TY  - JOUR
T1  - Adaptive CoMPI: Enhancing MPI based applications performance and scalability by using adaptive compression.
JF  - International Journal of High Performance Computing and Applications, 2010. Sage
Y1  - 2010
A1  - Rosa Filgueira
A1  - David E. Singh
A1  - Alejandro Calderón
A1  - Félix García Carballeira
A1  - Jesús Carretero
AB  - This paper presents an optimization of MPI communication, called Adaptive-CoMPI, based on runtime compression of MPI messages exchanged by applications. The technique developed can be used for any application, because its implementation is transparent for the user, and integrates different compression algorithms for both MPI collective and point-to-point primitives. Furthermore, compression is turned on and off and the most appropriate compression algorithms are selected at runtime, depending on the characteristics of each message, the network behavior, and compression algorithm behavior, following a runtime adaptive strategy. Our system can be optimized for a specific application, through a guided strategy, to reduce the runtime strategy overhead. Adaptive-CoMPI has been validated using several MPI benchmarks and real HPC applications. Results show that, in most cases, by using adaptive compression, communication time is reduced, enhancing application performance and scalability.
IS  - 25 (3)
ER  - 

TY  - JOUR
T1  - Comparing Clinical Decision Support Systems for Recruitment in Clinical Trials
JF  - Journal of Medical Informatics
Y1  - 2010
A1  - Marc Cuggia
A1  - Paolo Besana
A1  - David Glasspool.
ER  - 

TY  - JOUR
T1  - Dynamic-CoMPI: Dynamic optimization techniques for MPI parallel applications.
JF  - The Journal of Supercomputing.
Y1  - 2010
A1  - Rosa Filgueira
A1  - Jesús Carretero
A1  - David E. Singh
A1  - Alejandro Calderón
A1  - Alberto Nunez
KW  - Adaptive systems
KW  - Clusters architectures
KW  - Collective I/O
KW  - Compression algorithms
KW  - Heuristics
KW  - MPI library - Parallel techniques
AB  - This work presents an optimization of MPI communications, called Dynamic-CoMPI, which uses two techniques in order to reduce the impact of communications and non-contiguous I/O requests in parallel applications. These techniques are independent of the application and complementaries to each other. The first technique is an optimization of the Two-Phase collective I/O technique from ROMIO, called Locality aware strategy for Two-Phase I/O (LA-Two-Phase I/O). In order to increase the locality of the file accesses, LA-Two-Phase I/O employs the Linear Assignment Problem (LAP) for finding an optimal I/O data communication schedule. The main purpose of this technique is the reduction of the number of communications involved in the I/O collective operation. The second technique, called Adaptive-CoMPI, is based on run-time compression of MPI messages exchanged by applications. Both techniques can be applied on every application, because both of them are transparent for the users. Dynamic-CoMPI has been validated by using several MPI benchmarks and real HPC applications. The results show that, for many of the considered scenarios, important reductions in the execution time are achieved by reducing the size and the number of the messages. Additional benefits of our approach are the reduction of the total communication time and the network contention, thus enhancing, not only performance, but also scalability.
PB  - Springer
ER  - 

TY  - JOUR
T1  - An open source toolkit for medical imaging de-identification
JF  - European Radiology
Y1  - 2010
A1  - Rodríguez, David
A1  - Carpenter, Trevor K.
A1  - van Hemert, Jano I.
A1  - Wardlaw, Joanna M.
KW  - Anonymisation
KW  - Data Protection Act (DPA)
KW  - De-identification
KW  - Digital Imaging and Communications in Medicine (DICOM)
KW  - Privacy policies
KW  - Pseudonymisation
KW  - Toolkit
AB  - Objective    Medical imaging acquired for clinical purposes can have several legitimate secondary uses in research projects and teaching libraries. No commonly accepted solution for anonymising these images exists because the amount of personal data that should be preserved varies case by case. Our objective is to provide a flexible mechanism for anonymising Digital Imaging and Communications in Medicine (DICOM) data that meets the requirements for deployment in multicentre trials.  Methods    We reviewed our current de-identification practices and defined the relevant use cases to extract the requirements for the de-identification process. We then used these requirements in the design and implementation of the toolkit. Finally, we tested the toolkit taking as a reference those requirements, including a multicentre deployment.  Results    The toolkit successfully anonymised DICOM data from various sources. Furthermore, it was shown that it could forward anonymous data to remote destinations, remove burned-in annotations, and add tracking information to the header. The toolkit also implements the DICOM standard confidentiality mechanism.  Conclusion    A DICOM de-identification toolkit that facilitates the enforcement of privacy policies was developed. It is highly extensible, provides the necessary flexibility to account for different de-identification requirements and has a low adoption barrier for new users.
VL  - 20
UR  - http://www.springerlink.com/content/j20844338623m167/
IS  - 8
ER  - 

TY  - CONF
T1  - Advanced Data Mining and Integration Research for Europe
T2  - All Hands Meeting 2009
Y1  - 2009
A1  - Atkinson, M.
A1  - Brezany, P.
A1  - Corcho, O.
A1  - Han, L
A1  - van Hemert, J.
A1  - Hluchy, L.
A1  - Hume, A.
A1  - Janciak, I.
A1  - Krause, A.
A1  - Snelling, D.
A1  - Wöhrer, A.
AB  - There is a rapidly growing wealth of data [1]. The number of sources of data is increasing,  while, at the same time, the diversity, complexity and scale of these data resources are also increasing  dramatically. This cornucopia of data oers much potential; a combinatorial explosion of opportunities  for knowledge discovery, improved decisions and better policies. Today, most of these opportunities are  not realised because composing data from multiple sources and extracting information is too dicult.  Every business, organisation and government faces problems that can only be addressed successfully if  we improve our techniques for exploiting the data we gather.
JF  - All Hands Meeting 2009
CY  - Oxford
ER  - 

TY  - CONF
T1  - CoMPI: Enhancing MPI Based Applications Performance and Scalability Using Run-Time Compression.
T2  - EUROPVM/MPI 2009.Espoo, Finland. September 2009
Y1  - 2009
A1  - Rosa Filgueira
A1  - David E. Singh
A1  - Alejandro Calderón
A1  - Jesús Carretero
AB  - This paper presents an optimization of MPI communications, called CoMPI, based on run-time compression of MPI messages exchanged by applications. A broad number of compression algorithms have been fully implemented and tested for both MPI collective and point to point primitives. In addition, this paper presents a study of several compression algorithms that can be used for run-time compression, based on the datatype used by applications. This study has been validated by using several MPI benchmarks and real HPC applications. Show that, in most of the cases, using compression reduces the application communication time enhancing application performance and scalability. In this way, CoMPI obtains important improvements in the overall execution time for many of the considered scenarios.
JF  - EUROPVM/MPI 2009.Espoo, Finland. September 2009
PB  - Springer
CY  - Espoo. Finland
VL  - 5759/2009
ER  - 

TY  - Generic
T1  - Crossing boundaries: computational science, e-Science and global e-Infrastructure I
T2  - All Hands meeting 2008
Y1  - 2009
A1  - Coveney, P. V.
A1  - Atkinson, M. P.
ED  - Coveney, P. V.
ED  - Atkinson, M. P.
JF  - All Hands meeting 2008
T3  - Philosophical Transactions of the Royal Society Series A
PB  - Royal Society Publishing
CY  - Edinburgh
VL  - 367
UR  - http://rsta.royalsocietypublishing.org/content/367/1897.toc
ER  - 

TY  - Generic
T1  - Crossing boundaries: computational science, e-Science and global e-Infrastructure  II
T2  - All Hands Meeting 2008
Y1  - 2009
A1  - Coveney, P. V.
A1  - Atkinson, M. P.
ED  - Coveney, P. V.
ED  - Atkinson, M. P.
JF  - All Hands Meeting 2008
T3  - Philosophical Transactions of the Royal Society Series A
PB  - Royal Society Publishing
CY  - Edinburgh
VL  - 367
UR  - http://rsta.royalsocietypublishing.org/content/367/1898.toc
ER  - 

TY  - JOUR
T1  - Preface. Crossing boundaries: computational science, e-Science and global e-Infrastructure
JF  - Philosophical Transactions of the Royal Society Series A
Y1  - 2009
A1  - Coveney, P. V.
A1  - Atkinson, M. P.
PB  - Royal Society Publishing
VL  - 367
ER  - 

TY  - JOUR
T1  - A Strategy for Research and Innovation in the Century of Information
JF  - Prometheus
Y1  - 2009
A1  - e-Science Directors’ Forum Strategy Working Group
A1  - Atkinson, M.
A1  - Britton, D.
A1  - Coveney, P.
A1  - De Roure, D
A1  - Garnett, N.
A1  - Geddes, N.
A1  - Gurney, R.
A1  - Haines, K.
A1  - Hughes, L.
A1  - Ingram, D.
A1  - Jeffreys, P.
A1  - Lyon, L.
A1  - Osborne, I.
A1  - Perrott, P.
A1  - Procter. R.
A1  - Rusbridge, C.
AB  - More data will be produced in the next five years than in the entire history of human kind, a digital deluge that marks the beginning of the Century of Information. Through a year‐long consultation with UK researchers, a coherent strategy has been developed, which will nurture Century‐of‐Information Research (CIR); it crystallises the ideas developed by the e‐Science Directors’ Forum Strategy Working Group. This paper is an abridged version of their latest report which can be found at: http://wikis.nesc.ac.uk/escienvoy/Century_of_Information_Research_Strategy which also records the consultation process and the affiliations of the authors. This document is derived from a paper presented at the Oxford e‐Research Conference 2008 and takes into account suggestions made in the ensuing panel discussion.    The goals of the CIR Strategy are to facilitate the growth of UK research and innovation that is data and computationally intensive and to develop a new culture of ‘digital‐systems judgement’ that will equip research communities, businesses, government and society as a whole, with the skills essential to compete and prosper in the Century of Information. The CIR Strategy identifies a national requirement for a balanced programme of coordination, research, infrastructure, translational investment and education to empower UK researchers, industry, government and society. The Strategy is designed to deliver an environment which meets the needs of UK researchers so that they can respond agilely to challenges, can create knowledge and skills, and can lead new kinds of research. It is a call to action for those engaged in research, those providing data and computational facilities, those governing research and those shaping education policies. The ultimate aim is to help researchers strengthen the international competitiveness of the UK research base and increase its contribution to the economy.    The objectives of the Strategy are to better enable UK researchers across all disciplines to contribute world‐leading fundamental research; to accelerate the translation of research into practice; and to develop improved capabilities, facilities and context for research and innovation. It envisages a culture that is better able to grasp the opportunities provided by the growing wealth of digital information. Computing has, of course, already become a fundamental tool in all research disciplines. The UK e‐Science programme (2001–06)—since emulated internationally—pioneered the invention and use of new research methods, and a new wave of innovations in digital‐information technologies which have enabled them. The Strategy argues that the UK must now harness and leverage its own, plus the now global, investment in digital‐information technology in order to spread the benefits as widely as possible in research, education, industry and government.    Implementing the Strategy would deliver the computational infrastructure and its benefits as envisaged in the Science & Innovation Investment Framework 2004–2014 (July 2004), and in the reports developing those proposals.    To achieve this, the Strategy proposes the following actions:  	    1. support the continuous innovation of digital‐information research methods;  2. provide easily used, pervasive and sustained e‐Infrastructure for all research;  3. enlarge the productive research community which exploits the new methods efficiently;  4. generate capacity, propagate knowledge and develop skills via new curricula; and  5. develop coordination mechanisms to improve the opportunities for interdisciplinary research and to make digital‐infrastructure provision more cost effective.    To gain the best value for money strategic coordination is required across a broad spectrum of stakeholders. A coherent strategy is essential in order to establish and sustain the UK as an international leader of well‐curated national data assets and computational infrastructure, which is expertly used to shape policy, support decisions, empower researchers and to roll out the results to the wider benefit of society. The value of data as a foundation for wellbeing and a sustainable society must be appreciated; national resources must be more wisely directed to the collection, curation, discovery, widening access, analysis and exploitation of these data. Every researcher must be able to draw on skills, tools and computational resources to develop insights, test hypotheses and translate inventions into productive use, or to extract knowledge in support of governmental decision making. This foundation plus the skills developed will launch significant advances in research, in business, in professional practice and in government with many consequent benefits for UK citizens. The Strategy presented here addresses these complex and interlocking requirements.
VL  - 27
ER  - 

TY  - CONF
T1  - Using architectural simulation models to aid the design of data intensive application
T2  - The Third International Conference on Advanced Engineering Computing and Applications in Sciences (ADVCOMP 2009)
Y1  - 2009
A1  - Javier Fernández
A1  - Liangxiu Han
A1  - Alberto Nuñez
A1  - Jesus Carretero
A1  - van Hemert, Jano
JF  - The Third International Conference on Advanced Engineering Computing and Applications in Sciences (ADVCOMP 2009)
PB  - IEEE Computer Society
CY  - Sliema, Malta
ER  - 

TY  - CHAP
T1  - Contraction-Based Heuristics to Improve the Efficiency of Algorithms Solving the Graph Colouring Problem
T2  - Studies in Computational Intelligence
Y1  - 2008
A1  - Juhos, I.
A1  - van Hemert, J. I.
ED  - Cotta, C.
ED  - van Hemert, J. I.
KW  - constraint satisfaction
KW  - evolutionary computation
KW  - graph colouring
JF  - Studies in Computational Intelligence
PB  - Springer
ER  - 

TY  - CONF
T1  - Data Locality Aware Strategy for Two-Phase Collective I/O
T2  - VECPAR
Y1  - 2008
A1  - Rosa Filgueira
A1  - David E. Singh
A1  - Juan Carlos Pichel
A1  - Florin Isaila
A1  - Jesús Carretero
JF  - VECPAR
ER  - 

TY  - JOUR
T1  - Distributed Computing Education, Part 3: The Winter School Online Experience
JF  - Distributed Systems Online
Y1  - 2008
A1  - Low, B.
A1  - Cassidy, K.
A1  - Fergusson, D.
A1  - Atkinson, M.
A1  - Vander Meer, E.
A1  - McGeever, M.
AB  - The International Summer Schools in Grid Computing (ISSGC) have provided numerous international students with the opportunity to learn grid systems, as detailed in part 2 of this series (http://doi.ieeecomputersociety.org/10.1109/MDSO.2008.20). The International Winter School on Grid Computing 2008 (IWSGC 08) followed the successful summer schools, opening up the ISSGC experience to a wider range of students because of its online format. The previous summer schools made it clear that many students found the registration and travel costs and the time requirements prohibitive. The EU FP6 ICEAGE project held the first winter school from 6 February to 12 March 2008. The winter school repurposed summer school materials and added resources such as the ICEAGE digital library and summer-school-tested t-Infrastructures such as GILDA (Grid INFN Laboratory for Dissemination Activities).    The winter schools shared the goals of the summer school, which emphasized disseminating grid knowledge. The students act as multipliers, spreading the skills and knowledge they acquired at the winter school to their colleagues to build strong and enthusiastic local grid communities.
PB  - IEEE Computer Society
VL  - 9
UR  - http://ieeexplore.ieee.org/stamp/stamp.jsp?tp=&arnumber=4659260
IS  - 9
ER  - 

TY  - JOUR
T1  - Distributed Computing Education, Part 5: Coming to Terms with Intellectual Property Rights
JF  - Distributed Systems Online
Y1  - 2008
A1  - Boon Low
A1  - Kathryn Cassidy
A1  - Fergusson, David
A1  - Malcolm Atkinson
A1  - Elizabeth Vander Meer
A1  - Mags McGeever
AB  - In part 1 of this series on distributed computing education, we introduced a list of components important for teaching environments. We outlined the first three components, which included development of materials for education, education for educators and teaching infrastructures, identifying current practice, challenges, and opportunities for provision. The final component, a supportive policy framework that encourages cooperation and sharing, includes the need to manage intellectual property rights (IPR).
PB  - IEEE Computer Society
VL  - 9
UR  - http://ieeexplore.ieee.org/stamp/stamp.jsp?tp=&arnumber=4755177
IS  - 12
ER  - 

TY  - Generic
T1  - Evolutionary Computation in Combinatorial Optimization, 8th European Conference
T2  - Lecture Notes in Computer Science
Y1  - 2008
A1  - van Hemert, Jano
A1  - Cotta, Carlos
ED  - van Hemert, Jano
ED  - Cotta, Carlos
KW  - evolutionary computation
AB  - Metaheuristics have shown to be effective for difficult combinatorial  optimization problems appearing in various industrial, economical, and  scientific domains. Prominent examples of metaheuristics are evolutionary  algorithms, tabu search, simulated annealing, scatter search, memetic  algorithms, variable neighborhood search, iterated local search, greedy  randomized adaptive search procedures, ant colony optimization and estimation  of distribution algorithms. Problems solved successfully include scheduling,  timetabling, network design, transportation and distribution, vehicle routing,  the travelling salesman problem,  packing and cutting, satisfiability and  general mixed integer programming.    EvoCOP began in 2001 and has been held annually since then. It is  the first event specifically dedicated to the application of  evolutionary computation and related methods to combinatorial  optimization problems. Originally held as a workshop, EvoCOP became  a conference in 2004. The events gave researchers an excellent  opportunity to present their latest research and to discuss current  developments and applications. Following  the general trend of hybrid metaheuristics and diminishing  boundaries between the different classes of metaheuristics, EvoCOP  has broadened its scope over the last years and invited submissions  on any kind of metaheuristic for combinatorial optimization.
JF  - Lecture Notes in Computer Science
PB  - Springer
VL  - LNCS 4972
ER  - 

TY  - CONF
T1  - Exploiting data compression in collective I/O techniques.
T2  - Cluster Computing 2008.
Y1  - 2008
A1  - Rosa Filgueira
A1  - David E. Singh
A1  - Juan Carlos Pichel
A1  - Jesús Carretero
JF  - Cluster Computing 2008.
CY  - Tsukuba, Japand.
SN  - 978-1-4244-2639-3
ER  - 

TY  - CONF
T1  - Graph Colouring Heuristics Guided by Higher Order Graph Properties
T2  - Lecture Notes in Computer Science
Y1  - 2008
A1  - Juhos, Istv\'{a}n
A1  - van Hemert, Jano
ED  - van Hemert, Jano
ED  - Cotta, Carlos
KW  - evolutionary computation
KW  - graph colouring
AB  - Graph vertex colouring can be defined in such a way where colour assignments are substituted by vertex contractions. We present various hyper-graph representations for the graph colouring problem all based on the approach where vertices are merged into groups. In this paper, we show this provides a uniform and compact way to define algorithms, both of a complete or a heuristic nature. Moreover, the representation provides information useful to guide algorithms during their search. In this paper we focus on the quality of solutions obtained by graph colouring heuristics that make use of higher order properties derived during the search. An evolutionary algorithm is used to search permutations of possible merge orderings.
JF  - Lecture Notes in Computer Science
PB  - Springer
VL  - 4972
ER  - 

TY  - JOUR
T1  - A Grid infrastructure for parallel and interactive applications
JF  - Computing and Informatics
Y1  - 2008
A1  - Gomes, J.
A1  - Borges, B.
A1  - Montecelo, M.
A1  - David, M.
A1  - Silva, B.
A1  - Dias, N.
A1  - Martins, JP
A1  - Fernandez, C.
A1  - Garcia-Tarres, L. ,
A1  - Veiga, C.
A1  - Cordero, D.
A1  - Lopez, J.
A1  - J Marco
A1  - Campos, I.
A1  - Rodríguez, David
A1  - Marco,  R.
A1  - Lopez, A.
A1  - Orviz, P.
A1  - Hammad, A.
VL  - 27
IS  - 2
ER  - 

TY  - JOUR
T1  - The interactive European Grid: Project objectives and achievements
JF  - Computing and Informatics
Y1  - 2008
A1  - J Marco
A1  - Campos, I.
A1  - Coterillo, I.
A1  - Diaz, I.
A1  - Lopez, A.
A1  - Marco,  R.
A1  - Martinez-Rivero, C.
A1  - Orviz, P.
A1  - Rodríguez, David
A1  - Gomes, J.
A1  - Borges, G.
A1  - Montecelo, M.
A1  - David, M.
A1  - Silva, B.
A1  - Dias, N.
A1  - Martins, JP
A1  - Fernandez, C.
A1  - Garcia-Tarres, L.
VL  - 27
IS  - 2
ER  - 

TY  - BOOK
T1  - Recent Advances in Evolutionary Computation for Combinatorial Optimization
T2  - Studies in Computational Intelligence
Y1  - 2008
A1  - Cotta, Carlos
A1  - van Hemert, Jano
AB  - Combinatorial optimisation is a ubiquitous discipline whose usefulness spans vast applications domains. The intrinsic complexity of most combinatorial optimisation problems makes classical methods unaffordable in many cases. To acquire practical solutions to these problems requires the use of metaheuristic approaches that trade completeness for pragmatic effectiveness. Such approaches are able to provide optimal or quasi-optimal solutions to a plethora of difficult combinatorial optimisation problems.    The application of metaheuristics to combinatorial optimisation is an active field in which new theoretical developments, new algorithmic models, and new application areas are continuously emerging. This volume presents recent advances in the area of metaheuristic combinatorial optimisation, with a special focus on evolutionary computation methods. Moreover, it addresses local search methods and hybrid approaches. In this sense, the book includes cutting-edge theoretical, methodological, algorithmic and applied developments in the field, from respected experts and with a sound perspective.
JF  - Studies in Computational Intelligence
PB  - Springer
VL  - 153
SN  - 978-3-540-70806-3
UR  - http://www.springer.com/engineering/book/978-3-540-70806-3
ER  - 

TY  - CONF
T1  - Accessing Data in Grids Using OGSA-DAI
T2  - Knowledge and Data Management in Grids
Y1  - 2007
A1  - Chue Hong, N. P.
A1  - Antonioletti, M.
A1  - Karasavvas, K. A.
A1  - Atkinson, M.
ED  - Talia, D.
ED  - Bilas, A.
ED  - Dikaiakos, M.
AB  - The grid provides a vision in which resources, including storage and data, can be shared across organisational boundaries. The original emphasis of grid computing lay in the sharing of computational resources but technological and scientific advances have led to an ongoing data explosion in many fields. However, data is stored in many different storage systems and data formats, with different schema, access rights, metadata attributes, and ontologies all of which are obstacles to the access, integration and management of this information.    In this chapter we examine some of the ways in which these differences can be addressed by grid technology to enable the meaningful sharing of data. In particular, we present an overview of the OGSA-DAI (Open Grid Service Architecture - Data Access and Integration) software, which provides a uniform, extensible framework for accessing structured and semi-structured data and provide some examples of its use in other projects. The open-source OGSA-DAI software is freely available from http://www.ogsadai.org.uk.
JF  - Knowledge and Data Management in Grids
SN  - 978-0-387-37830-5
UR  - http://www.springer.com/computer/communication+networks/book/978-0-387-37830-5
ER  - 

TY  - CHAP
T1  - COBrA and COBrA-CT: Ontology Engineering Tools
T2  - Anatomy Ontologies for Bioinformatics: Principles and Practice
Y1  - 2007
A1  - Stuart Aitken
A1  - Yin Chen
ED  - Albert Burger
ED  - Duncan Davidson
ED  - Richard Baldock
AB  - COBrA is a Java-based ontology editor for bio-ontologies and anatomies that dif-   fers from other editors by supporting the linking of concepts between two ontologies, and   providing sophisticated analysis and verification functions. In addition to the Gene Ontology   and Open Biology Ontologies formats, COBrA can import and export ontologies in the Se-   mantic Web formats RDF, RDFS and OWL.   COBrA is being re-engineered as a Prot  ́eg  ́e plug-in, and complemented by an ontology   server and a tool for the management of ontology versions and collaborative ontology de-   velopment. We describe both the original COBrA tool and the current developments in this   chapter.
JF  - Anatomy Ontologies for Bioinformatics: Principles and Practice
PB  - Springer
SN  - ISBN-10:1846288843
UR  - http://www.amazon.ca/Anatomy-Ontologies-Bioinformatics-Principles-Practice/dp/1846288843
ER  - 

TY  - Generic
T1  - Evolutionary Computation in Combinatorial Optimization, 7th European Conference
T2  - Lecture Notes in Computer Science
Y1  - 2007
A1  - Cotta, Carlos
A1  - van Hemert, Jano
ED  - Carlos Cotta
ED  - van Hemert, Jano
KW  - evolutionary computation
AB  - Metaheuristics have often been shown to be effective for difficult combinatorial   optimization problems appearing in various industrial, economical, and scientific   domains. Prominent examples of metaheuristics are evolutionary algorithms,   simulated annealing, tabu search, scatter search, memetic algorithms, variable   neighborhood search, iterated local search, greedy randomized adaptive search   procedures, estimation of distribution algorithms, and ant colony optimization.   Successfully solved problems include scheduling, timetabling, network design,   transportation and distribution, vehicle routing, the traveling salesman problem,   satisfiability, packing and cutting, and general mixed integer programming.     EvoCOP began in 2001 and has been held annually since then. It was the   first event specifically dedicated to the application of evolutionary computation   and related methods to combinatorial optimization problems. Originally held as   a workshop, EvoCOP became a conference in 2004. The events gave researchers   an excellent opportunity to present their latest research and to discuss current   developments and applications as well as providing for improved interaction   between members of this scientific community. Following the general trend of   hybrid metaheuristics and diminishing boundaries between the different classes   of metaheuristics, EvoCOP has broadened its scope over the last years and   invited submissions on any kind of metaheuristic for combinatorial optimization.
JF  - Lecture Notes in Computer Science
PB  - Springer
VL  - LNCS 4446
UR  - http://springerlink.metapress.com/content/105633/
ER  - 

TY  - CONF
T1  - Grid Enabling Your Data Resources with OGSA-DAI
T2  - Applied Parallel Computing. State of the Art in Scientific Computing
Y1  - 2007
A1  - Antonioletti, M.
A1  - Atkinson, M.
A1  - Chue Hong, N. P.
A1  - Dobrzelecki, B.
A1  - Hume, A. C.
A1  - Jackson, M.
A1  - Karasavvas, K.
A1  - Krause, A.
A1  - Schopf, J. M.
A1  - Sugden. T.
A1  - Theocharopoulos, E.
JF  - Applied Parallel Computing. State of the Art in Scientific Computing
T3  - Lecture Notes in Computer Science
VL  - 4699
ER  - 

TY  - CONF
T1  - Interaction as a Grounding for Peer to Peer Knowledge Sharing
T2  - Advances in Web Semantics
Y1  - 2007
A1  - Robertson, D.
A1  - Walton, C.
A1  - Barker, A.
A1  - Besana, P.
A1  - Chen-Burger, Y.
A1  - Hassan, F.
A1  - Lambert, D.
A1  - Li, G.
A1  - McGinnis, J
A1  - Osman, N.
A1  - Bundy, A.
A1  - McNeill, F.
A1  - van Harmelen, F.
A1  - Sierra, C.
A1  - Giunchiglia, F.
JF  - Advances in Web Semantics
PB  - LNCS-IFIP
VL  - 1
ER  - 

TY  - CONF
T1  - Managing the transition from OBO to OWL: The COBrA-CT Bio-Ontology Tools
T2  - UK e-Science Al l Hands Meeting 2007
Y1  - 2007
A1  - S. Aitken
A1  - Y. Chen
KW  - Bio-ontology, Grid, OBO, OWL
AB  - This paper presents the COBrA-CT ontology tools, which include an ontology server database and  version manager client tool for collaborative ontology development, and an editor for bio-ontologies that are represented in the Web Ontology Language (OWL) format. The ontology server  uses OGSA-DAI Grid technology to provide access to the ontology server database. These tools  implement the agreed standard for representing Open Biomedical Ontologies (OBO) in OWL and  interoperate with other tools developed for this standard. Such tools are essential for the uptake of  OWL in the biomedical ontology community.
JF  - UK e-Science Al l Hands Meeting 2007
CY  - Nottingham, UK
ER  - 

TY  - JOUR
T1  - OBO Explorer: An Editor for Open Biomedical Ontologies in OWL
JF  - Bioinformatics
Y1  - 2007
A1  - Stuart Aitken
A1  - Yin Chen
A1  - Jonathan Bard
AB  - To clarify the semantics, and take advantage of tools and algorithms developed for the Semantic Web, a mapping from the Open Biomedical Ontologies (OBO) format to the Web Ontology Language (OWL) has been established. We present an ontology editor that allows end users to work directly with this OWL representation of OBO format ontologies.
PB  - Oxford Journals
UR  - http://bioinformatics.oxfordjournals.org/cgi/content/abstract/btm593?
ER  - 

TY  - CONF
T1  - Optimization and evaluation of parallel I/O in BIPS3D parallel irregular application
T2  - IPDPS
Y1  - 2007
A1  - Rosa Filgueira
A1  - David E. Singh
A1  - Florin Isaila
A1  - Jesús Carretero
A1  - Antonio Garcia Loureiro
JF  - IPDPS
ER  - 

TY  - CONF
T1  - Transaction-Based Grid Database Replication
T2  - UK e-Science Al l Hands Meeting 2007
Y1  - 2007
A1  - Y. Chen
A1  - D. Berry
A1  - P. Dantressangle
KW  - Grid, Replication, Transaction-based, OGSA-DAI
AB  - We present a framework for grid database replication. Data replication is one of the most useful  strategies to achieve high levels of availability and fault tolerance as well as minimal access time in  grids. It is commonly demanded by many grid applications. However, most existing grid replication  systems only deal with read-only files. By contrast, several relational database vendors provide  tools that offer transaction-based replication, but the capabilities of these products are insufficient to  address grid issues. They lack scalability and cannot cope with the heterogeneous nature of grid  resources.  Our approach uses existing grid mechanisms to provide a metadata registry and to make initial  replicas of data resources. We then define high-level APIs for managing transaction-based  replication. These APIs can be mapped to a variety of relational database replication mechanisms  allowing us to use existing vendor-specific solutions. The next stage in the project will use OGSA-  DAI to manage replication across multiple domains. In this way, our framework can support  transaction-based database synchronisation that maintains consistency in a data-intensive, large-  scale distributed, disparate networking environment.
JF  - UK e-Science Al l Hands Meeting 2007
CY  - Nottingham, UK
ER  - 

TY  - CHAP
T1  - Knowledge and Data Management in Grids, CoreGRID
T2  - Euro-Par'06 Proceedings of the CoreGRID 2006, UNICORE Summit 2006, Petascale Computational Biology and Bioinformatics conference on Parallel processing
Y1  - 2006
A1  - Chue Hong, N. P.
A1  - Antonioletti, M.
A1  - Karasavvas, K. A.
A1  - Atkinson, M.
ED  - Lehner, W.
ED  - Meyer, N.
ED  - Streit, A.
ED  - Stewart, C.
JF  - Euro-Par'06 Proceedings of the CoreGRID 2006, UNICORE Summit 2006, Petascale Computational Biology and Bioinformatics conference on Parallel processing
T3  - Lecture Notes in Computer Science
PB  - Springer
CY  - Berlin, Germany
VL  - 4375
SN  - 978-3-540-72226-7
UR  - http://www.springer.com/computer/communication+networks/book/978-3-540-72226-7
ER  - 

TY  - JOUR
T1  - The design and implementation of Grid database services in OGSA-DAI
JF  - Concurrency - Practice and Experience
Y1  - 2005
A1  - Antonioletti, Mario
A1  - Atkinson, Malcolm P.
A1  - Baxter, Robert M.
A1  - Borley, Andrew
A1  - Hong, Neil P. Chue
A1  - Collins, Brian
A1  - Hardman, Neil
A1  - Hume, Alastair C.
A1  - Knox, Alan
A1  - Mike Jackson
A1  - Krause, Amrey
A1  - Laws, Simon
A1  - Magowan, James
A1  - Pato
VL  - 17
ER  - 

TY  - CONF
T1  - Evolutionary Transitions as a Metaphor for Evolutionary Optimization
T2  - LNAI 3630
Y1  - 2005
A1  - Defaweux, A.
A1  - Lenaerts, T.
A1  - van Hemert, J. I.
ED  - M. Capcarrere
ED  - A. A. Freitas
ED  - P. J. Bentley
ED  - C. G. Johnson
ED  - J. Timmis
KW  - constraint satisfaction
KW  - transition models
AB  - This paper proposes a computational model for solving optimisation problems that mimics the principle of evolutionary transitions in individual complexity. More specifically it incorporates mechanisms for the emergence of increasingly complex individuals from the interaction of  more simple ones. The biological principles for transition are outlined and mapped onto  an evolutionary computation context.  The class of binary constraint satisfaction problems is used to illustrate the transition mechanism.
JF  - LNAI 3630
PB  - Springer-Verlag
SN  - 3-540-28848-1
ER  - 

TY  - Generic
T1  - Experience with the international testbed in the crossgrid project
T2  - Advances in Grid Computing-EGC 2005
Y1  - 2005
A1  - Gomes, J.
A1  - David, M.
A1  - Martins, J.
A1  - Bernardo, L.
A1  - A García
A1  - Hardt, M.
A1  - Kornmayer, H.
A1  - Marco, Jesus
A1  - Marco,  Rafael
A1  - Rodríguez, David
A1  - Diaz, Irma
A1  - Cano, Daniel
A1  - Salt, J.
A1  - Gonzalez, S.
A1  - J Sánchez
A1  - Fassi, F.
A1  - Lara, V.
A1  - Nyczyk, P.
A1  - Lason, P.
A1  - Ozieblo, A.
A1  - Wolniewicz, P.
A1  - Bluj, M.
A1  - K Nawrocki
A1  - A Padee
A1  - W Wislicki
ED  - Peter M. A. Sloot, Alfons G. Hoekstra, Thierry Priol, Alexander Reinefeld
ED  - Marian Bubak
JF  - Advances in Grid Computing-EGC 2005
T3  - LNCS
PB  - Springer Berlin/Heidelberg
CY  - Amsterdam
VL  - 3470
ER  - 

TY  - Generic
T1  - Genetic Programming, Proceedings of the 8th European Conference
T2  - Lecture Notes in Computer Science
Y1  - 2005
A1  - Keijzer, M.
A1  - Tettamanzi, A.
A1  - Collet, P.
A1  - van Hemert, J.
A1  - Tomassini, M.
ED  - M. Keijzer
ED  - A. Tettamanzi
ED  - P. Collet
ED  - van Hemert, J.
ED  - M. Tomassini
KW  - evolutionary computation
JF  - Lecture Notes in Computer Science
PB  - Springer
VL  - 3447
SN  - 3-540-25436-6
UR  - http://www.springeronline.com/sgw/cda/frontpage/0,11855,3-40100-22-45347265-0,00.html?changeHeader=true
ER  - 

TY  - CONF
T1  - Organization of the International Testbed of the CrossGrid Project
T2  - Cracow Grid Workshop 2005
Y1  - 2005
A1  - Gomes, J.
A1  - David, M.
A1  - Martins, J.
A1  - Bernardo, L.
A1  - Garcia, A.
A1  - Hardt, M.
A1  - Kornmayer, H.
A1  - Marco,  Rafael
A1  - Rodríguez, David
A1  - Diaz, Irma
A1  - Cano, Daniel
A1  - Salt, J.
A1  - Gonzalez, S.
A1  - Sanchez, J.
A1  - Fassi, F.
A1  - Lara, V.
A1  - Nyczyk, P.
A1  - Lason, P.
A1  - Ozieblo, A.
A1  - Wolniewicz, P.
A1  - Bluj, M.
JF  - Cracow Grid Workshop 2005
ER  - 

TY  - JOUR
T1  - Specifying use case behavior with interaction models
JF  - Journal of Object Technology
Y1  - 2005
A1  - José Daniel Garcia
A1  - Jesús Carretero
A1  - José Maria Pérez
A1  - Félix García Carballeira
A1  - Rosa Filgueira
VL  - 4
ER  - 

TY  - CONF
T1  - Grid-Based Metadata Services
T2  - SSDBM
Y1  - 2004
A1  - Deelman, Ewa
A1  - Singh, Gurmeet Singh
A1  - Atkinson, Malcolm P.
A1  - Chervenak, Ann L.
A1  - Hong, Neil P. Chue
A1  - Kesselman, Carl
A1  - Patil, Sonal
A1  - Pearlman, Laura
A1  - Su, Mei-Hui
JF  - SSDBM
ER  - 

TY  - CONF
T1  - OGSA-DAI Status Report and Future Directions
T2  - All Hands Meeting 2004
Y1  - 2004
A1  - Antonioletti, Mario
A1  - Malcolm Atkinson
A1  - Rob Baxter
A1  - Borley, Andrew
A1  - Hong, Neil P. Chue
A1  - Collins, Brian
A1  - Jonathan Davies
A1  - Desmond Fitzgerald
A1  - Hardman, Neil
A1  - Hume, Alastair C.
A1  - Mike Jackson
A1  - Krause, Amrey
A1  - Laws, Simon
A1  - Paton, Norman W.
A1  - Tom Sugden
A1  - Watson, Paul
A1  - Mar
AB  - Data Access and Integration (DAI) of data resources, such as relational and XML databases, within a Grid context. Project members also participate in the development of DAI standards through the GGF DAIS WG. The standards that emerge through this effort will be adopted by OGSA-DAI once they have stabilised. The OGSA-DAI developers are also engaging with a growing user community to gather their data and functionality requirements. Several large projects are already using OGSA-DAI to provide their DAI capabilities. This paper presents a status report on OGSA-DAI activities since the last AHM and announces future directions. The OGSA-DAI software distribution and more information about the project is available from the project website at http://www.ogsadai.org.uk/.
JF  - All Hands Meeting 2004
CY  - Nottingham, UK
ER  - 

TY  - CONF
T1  - OGSA-DAI: Two Years On
T2  - GGF10
Y1  - 2004
A1  - Antonioletti, Mario
A1  - Malcolm Atkinson
A1  - Rob Baxter
A1  - Borley, Andrew
A1  - Neil Chue Hong
A1  - Collins, Brian
A1  - Jonathan Davies
A1  - Hardman, Neil
A1  - George Hicken
A1  - Ally Hume
A1  - Mike Jackson
A1  - Krause, Amrey
A1  - Laws, Simon
A1  - Magowan, James
A1  - Jeremy Nowell
A1  - Paton, Norman W.
A1  - Dave Pearson
A1  - To
AB  - The OGSA-DAI project has been producing Grid-enabled middleware for almost two years now, providing data access and integration capabilities to data resources, such as databases, within an OGSA context. In these two years, OGSA-DAI has been tracking rapidly evolving standards, managing changes in software dependencies, contributing to the standardisation process and liasing with a growing user community together with their associated data requirements. This process has imparted important lessons and raised a number of issues that need to be addressed if a middleware product is to be widely adopted. This paper examines the experiences of OGSA-DAI in implementing proposed standards, the likely impact that the still-evolving standards landscape will have on future implementations and how these affect uptake of the software. The paper also examines the gathering of requirements from and engagement with the Grid community, the difficulties of defining a process for the management and publishing of metadata, and whether relevant standards can be implemented in an efficient manner. The OGSA-DAI software distribution and more details about the project are available from the project Web site at http://www.ogsadai.org.uk/.
JF  - GGF10
CY  - Berlin, Germany
ER  - 

TY  - JOUR
T1  - Comparing Evolutionary Algorithms on Binary Constraint Satisfaction Problems
JF  - IEEE Transactions on Evolutionary Computation
Y1  - 2003
A1  - Craenen, B. G. W.
A1  - Eiben, A. E.
A1  - van Hemert, J. I.
KW  - constraint satisfaction
AB  - Constraint handling is not straightforward in evolutionary algorithms (EA) since the usual search operators, mutation and recombination, are `blind' to constraints. Nevertheless, the issue is highly relevant, for many challenging problems involve constraints. Over the last decade numerous EAs for solving constraint satisfaction problems (CSP) have been introduced and studied on various problems. The diversity of approaches and the variety of problems used to study the resulting algorithms prevents a fair and accurate comparison of these algorithms. This paper aligns related work by presenting a concise overview and an extensive performance comparison of all these EAs on a systematically generated test suite of random binary CSPs. The random problem instance generator is based on a theoretical model that fixes deficiencies of models and respective generators that have been formerly used in the Evolutionary Computing (EC) field.
VL  - 7
UR  - http://ieeexplore.ieee.org/xpl/abs_free.jsp?isNumber=27734&prod=JNL&arnumber=1237162&arSt=+424&ared=+444&arAuthor=+Craenen%2C+B.G.W.%3B++Eiben%2C+A.E.%3B++van+Hemert%2C+J.I.&arNumber=1237162&a_id0=1237161&a_id1=1237162&a_id2=1237163&a_id3=1237164&a_id4=12
ER  - 

TY  - RPRT
T1  - Computer Challenges to emerge from e-Science.
Y1  - 2003
A1  - Atkinson, M.
A1  - Crowcroft, J.
A1  - Goble, C.
A1  - Gurd, J.
A1  - Rodden, T.
A1  - Shadbolt, N.
A1  - Sloman, M.
A1  - Sommerville, I.
A1  - Storey, T.
AB  - The UK e-Science programme has initiated significant developments that allow networked grid technology to be used to form virtual colaboratories. The e-Science vision of a globally connected community has broader application than science with the same fundamental technologies being used to support eCommerce and e-Government.     The broadest vision of e-Science outlines a challenging research agenda for the computing community. New theories and models will be needed to provide a sound foundation for the tools used to specify, design, analyse and prove the properties of future grid technologies and applications. Fundamental research is needed in order to build a future e-Science infrastructure and to understand how to exploit the infrastructure to best effect.     A future infrastructure needs to be dynamic, universally available and promote trust. Realising this infrastructure will need new theories, methods and techniques to be developed and deployed. Although often not directly visible these fundamental infrastructure advances will provide the foundation for future scientific advancement, wealth generation and governance.     • We need to move from the current data focus to a semantic grid with facilities for the generation, support and traceability of knowledge.   • We need to make the infrastructure more available and more trusted by developing trusted ubiquitous systems.   • We need to reduce the cost of development by enabling the rapid customised assembly of services.   • We need to reduce the cost and complexity of managing the infrastructure by realising autonomic computing systems.
JF  - EPSRC
ER  - 

TY  - CHAP
T1  - Data Access, Integration, and Management
T2  - The Grid 2: Blueprint for a New Computing Infrastructure (2nd edition),
Y1  - 2003
A1  - Atkinson. M.
A1  - Chervenak, A. L.
A1  - Kunszt, P.
A1  - Narang, I.
A1  - Paton, N. W.
A1  - Pearson, D.
A1  - Shoshani, A.
A1  - Watson, P.
ED  - Foster, I.
ED  - Kesselman, C
JF  - The Grid 2: Blueprint for a New Computing Infrastructure (2nd edition),
PB  - Morgan Kaufmann
SN  - 1-55860-933-4
ER  - 

TY  - CONF
T1  - Dependable Grid Services
T2  - UK e-Science All Hands Meeting 2003, 2-4th September, Nottingham, UK
Y1  - 2003
A1  - Stuart Anderson
A1  - Yin Chen
A1  - Glen Dobson
A1  - Stephen Hall
A1  - Conrad Hughes
A1  - Yong Li
A1  - Sheng Qu
A1  - Ed Smith
A1  - Ian Sommerville
A1  - Ma Tiejun
ED  - Proceedings of UK e-Science All Hands Meeting 2003
AB  - The provision of dependable computer systems by deploying diverse, redundant components  in order to mask or provide recovery from component failures has mostly been restricted to  systems with very high criticality. In this paper we present an architecture and prototype implementation of an approach to providing such redundancy at low cost in service-based infrastructures. In particular we consider services that are supplied by composing a number of component  services and consider how service discovery, automatic monitoring and failure detection have the  potential to create composed services that are more dependable than might be possible using a  straightforward approach. The work is still in its early stages and so far no evaluation of the  approach has been carried out.
JF  - UK e-Science All Hands Meeting 2003, 2-4th September, Nottingham, UK
CY  - Nottingham, UK
ER  - 

TY  - CONF
T1  - The Design and Implementation of Grid Database Services in OGSA-DAI
T2  - All Hands Meeting 2003
Y1  - 2003
A1  - Ali Anjomshoaa
A1  - Antonioletti, Mario
A1  - Malcolm Atkinson
A1  - Rob Baxter
A1  - Borley, Andrew
A1  - Hong, Neil P. Chue
A1  - Collins, Brian
A1  - Hardman, Neil
A1  - George Hicken
A1  - Ally Hume
A1  - Knox, Alan
A1  - Mike Jackson
A1  - Krause, Amrey
A1  - Laws, Simon
A1  - Magowan, James
A1  - Charaka Palansuriya
A1  - Paton, Norman W.
AB  - This paper presents a high-level overview of the design and implementation of the core components of the OGSA-DAI project. It describes the design decisions made, the project’s interaction with the Data Access and Integration Working Group of the Global Grid Forum and provides an overview of implementation characteristics. Further details of the implementation are provided in the extensive documentation available from the project web site.
JF  - All Hands Meeting 2003
CY  - Nottingham, UK
ER  - 

TY  - JOUR
T1  - The pervasiveness of evolution in GRUMPS software
JF  - Softw., Pract. Exper.
Y1  - 2003
A1  - Evans, Huw
A1  - Atkinson, Malcolm P.
A1  - Brown, Margaret
A1  - Cargill, Julie
A1  - Crease, Murray
A1  - Draper, Steve
A1  - Gray, Philip D.
A1  - Thomas, Richard
VL  - 33
ER  - 

TY  - CONF
T1  - Comparing Classical Methods for Solving Binary Constraint Satisfaction Problems with State of the Art Evolutionary Computation
T2  - Springer Lecture Notes on Computer Science
Y1  - 2002
A1  - van Hemert, J. I.
ED  - S. Cagnoni
ED  - J. Gottlieb
ED  - E. Hart
ED  - M. Middendorf
ED  - G. Raidl
KW  - constraint satisfaction
AB  - Constraint Satisfaction Problems form a class of problems that are generally computationally difficult and have been addressed with many complete and heuristic algorithms. We present two complete algorithms, as well as two evolutionary algorithms, and compare them on randomly generated instances of binary constraint satisfaction prob-lems. We find that the evolutionary algorithms are less effective than the classical techniques.
JF  - Springer Lecture Notes on Computer Science
PB  - Springer-Verlag, Berlin
ER  - 

TY  - JOUR
T1  - A network traffic model based on the cascade process
JF  - Journal of Mini-Micro Computer System
Y1  - 2002
A1  - Liangxiu Han
A1  - yan Liu
A1  - Zhiwei Cen
VL  - 23
IS  - 12
ER  - 

TY  - JOUR
T1  - A new multifractal network traffic model
JF  - Journal of Chaos, solitons & fractals
Y1  - 2002
A1  - Liangxiu Han
A1  - Zhiwei Ceng
A1  - Chuanshan Gao
PB  - Elsevier Science
VL  - 13
IS  - 7
ER  - 

TY  - BOOK
T1  - GRUMPS Summer Anthology, 2001
Y1  - 2001
A1  - Atkinson, M.
A1  - Brown, M.
A1  - Cargill, J.
A1  - Crease, M.
A1  - Draper, S.
A1  - Evans, H.
A1  - Gray, P.
A1  - Mitchell, C.
A1  - Ritchie, M.
A1  - Thomas, R.
AB  - This is the first collection of papers from GRUMPS [http://grumps.dcs.gla.ac.uk]. The project only started up in February 2001, and this collection (frozen at 1 Sept 2001) shows that it got off to a productive start. Versions of some of these papers have been submitted to conferences and workshops: the website will have more information on publication status and history.  GRUMPS decided to begin with a first study, partly to help the team coalesce. This involved installing two pieces of software in a first year computing science lab: one (the "UAR") to record a large volume of student actions at a low level with a view to mining them later, another (the "LSS") directly designed to assist tutor-student interaction. Some of the papers derive from that, although more are planned. Results from this first study can be found on the website. The project also has a link to UWA in Perth, Western Australia, where related software has already been developed and used as described in one of the papers. Another project strand concerns using handsets in lecture theatres to support interactivity there, as two other papers describe. As yet unrepresented in this collection, GRUMPS will also be entering the bioinformatics application area.    The GRUMPS project operates on several levels. It is based in the field of Distributed Information Management (DIM), expecting to cover both mobile and static nodes, synchronous and detached clients, high and low volume data sources. The specific focus of the project (see the original proposal on the web site) is to address records of computational activity (where any such pre-existing usage might have extra record collection installed) and data experimentation, where the questions to be asked of the data emerge concurrently with data collection which will therefore be dynamically modifiable: a requirement that further pushes on the space of DIM. The level above concerns building and making usable tools for asking questions of the data, or rather of the activities that generate the data. Above that again is the application domain level: what the original computational activities serve, education and bioinformatics being two identified cases.  The GRUMPS team is therefore multidisciplinary, from DIM architecture researchers to educational evaluators. The mix of papers reflects this.
PB  - Academic Press
ER  - 

TY  - CHAP
T1  - Scalable and Recoverable Implementation of Object Evolution for the PJama1 Platform
T2  - Persistent Object Systems: Design, Implementation, and Use 9th International Workshop, POS-9 Lillehammer, Norway, September 6–8, 2000 Revised Papers
Y1  - 2001
A1  - Atkinson, M. P.
A1  - Dmitriev, M. A.
A1  - Hamilton, C.
A1  - Printezis, T.
ED  - Graham N. C.
ED  - Kirby, Alan Dearle
ED  - Dag I. K. Sjøberg
AB  - PJama1 is the latest version of an orthogonally persistent platform for Java. It depends on a new persistent object store, Sphere, and provides facilities for class evolution. This evolution technology supports an arbitrary set of changes to the classes, which may have arbitrarily large populations of persistent objects. We verify that the changes are safe. When there are format changes, we also convert all of the instances, while leaving their identities unchanged. We aspire to both very large persistent object stores and freedom for developers to specify arbitrary conversion methods in Java to convey information from old to new formats.    Evolution operations must be safe and the evolution cost should be approximately linear in the number of objects that must be reformatted. In order that these conversion methods can be written easily, we continue to present the pre-evolution state consistently to Java executions throughout an evolution. At the completion of applying all of these transformations, we must switch the store state to present only the post-evolution state, with object identity preserved. We present an algorithm that meets these requirements for eager, total conversion.    This paper focuses on the mechanisms built into Sphere to support safe, atomic and scalable evolution. We report our experiences in using this technology and include a preliminary set of performance measurements.
JF  - Persistent Object Systems: Design, Implementation, and Use 9th International Workshop, POS-9 Lillehammer, Norway, September 6–8, 2000 Revised Papers
T3  - Lecture Notes in Computer Science
PB  - Springer
VL  - 2135
UR  - http://www.springerlink.com/content/09hx07h9lw0p1h82/?p=2bc20319905146bab8ba93b2fcc8cc01&pi=23
ER  - 

TY  - CONF
T1  - Measurement and analysis of IP network traffic
T2  - In Proceedings of the 3th International Asia-Pacific Web Conference
Y1  - 2000
A1  - cen, Z
A1  - Gao, C
A1  - Cong S
A1  - Han, L
JF  - In Proceedings of the 3th International Asia-Pacific Web Conference
CY  - xi'an China
ER  - 

TY  - CHAP
T1  - SAW-ing EAs: adapting the fitness function for solving constrained problems
T2  - New ideas in optimization
Y1  - 1999
A1  - Eiben, A. E.
A1  - van Hemert, J. I.
ED  - D. Corne
ED  - M. Dorigo
ED  - F. Glover
KW  - constraint satisfaction
AB  - In this chapter we describe a problem independent method for treating constrain ts in an evolutionary algorithm. Technically, this method amounts to changing the defini tion of the fitness function during a run of an EA, based on feedback from the search pr ocess. Obviously, redefining the fitness function means redefining the problem to be sol ved. On the short term this deceives the algorithm making the fitness values deteriorate , but as experiments clearly indicate, on the long run it is beneficial. We illustrate t he power of the method on different constraint satisfaction problems and point out other application areas of this technique.
JF  - New ideas in optimization
PB  - McGraw-Hill, London
ER  -