TY  - Generic
T1  - Varpy: A python library for volcanology and rock physics data analysis. EGU2014-3699
Y1  - 2014
A1  - Rosa Filgueira
A1  - Malcolm Atkinson
A1  - Andrew Bell
A1  - Branwen Snelling
ER  - 

TY  - CONF
T1  - C2MS: Dynamic Monitoring and Management of Cloud Infrastructures
T2  - IEEE CloudCom
Y1  - 2013
A1  - Gary McGilvary
A1  - Josep Rius
A1  - Íñigo Goiri
A1  - Francesc Solsona
A1  - Barker, Adam
A1  - Atkinson, Malcolm P.
AB  - Server clustering is a common design principle employed by many organisations who require high availability, scalability and easier management of their infrastructure. Servers are typically clustered according to the service they provide whether it be the application(s) installed, the role of the server or server accessibility for example. In order to optimize performance, manage load and maintain availability, servers may migrate from one cluster group to another making it difficult for server monitoring tools to continuously monitor these dynamically changing groups. Server monitoring tools are usually statically configured and with any change of group membership requires manual reconfiguration; an unreasonable task to undertake on large-scale cloud infrastructures.   In this paper we present the Cloudlet Control and Management System (C2MS); a system for monitoring and controlling dynamic groups of physical or virtual servers within cloud infrastructures. The C2MS extends Ganglia - an open source scalable system performance monitoring tool - by allowing system administrators to define, monitor and modify server groups without the need for server reconfiguration. In turn administrators can easily monitor group and individual server metrics on large-scale dynamic cloud infrastructures where roles of servers may change frequently. Furthermore, we complement group monitoring with a control element allowing administrator-specified actions to be performed over servers within service groups as well as introduce further customized monitoring metrics. This paper outlines the design, implementation and evaluation of the C2MS.
JF  - IEEE CloudCom
CY  - Bristol, UK
ER  - 

TY  - JOUR
T1  - The Cloud Paradigm Applied to e-Health
JF  - BMC Med. Inf. {&} Decision Making
Y1  - 2013
A1  - Jordi Vilaplana
A1  - Francesc Solsona
A1  - Francesc Abella
A1  - Rosa Filgueira
A1  - Josep Rius Torrento
VL  - 13
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  - CONF
T1  - The demand for consistent web-based workflow editors
T2  - Proceedings of the 8th Workshop on Workflows in Support of Large-Scale Science
Y1  - 2013
A1  - Gesing, Sandra
A1  - Atkinson, Malcolm
A1  - Klampanos, Iraklis
A1  - Galea, Michelle
A1  - Berthold, Michael R.
A1  - Barbera, Roberto
A1  - Scardaci, Diego
A1  - Terstyanszky, Gabor
A1  - Kiss, Tamas
A1  - Kacsuk, Peter
KW  - web-based workflow editors
KW  - workflow composition
KW  - workflow interoperability
KW  - workflow languages and concepts
JF  - Proceedings of the 8th Workshop on Workflows in Support of Large-Scale Science
PB  - ACM
CY  - New York, NY, USA
SN  - 978-1-4503-2502-8
UR  - http://doi.acm.org/10.1145/2534248.2534260
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  - JOUR
T1  - Embedded systems for global e-Social Science: Moving computation rather than data
JF  - Future Generation Computer Systems
Y1  - 2013
A1  - Ashley D. Lloyd
A1  - Terence M. Sloan
A1  - Antonioletti, Mario
A1  - Gary McGilvary
AB  - There is a wealth of digital data currently being gathered by commercial and private concerns that could supplement academic research. To unlock this data it is important to gain the trust of the companies that hold the data as well as showing them how they may benefit from this research. Part of this trust is gained through established reputation and the other through the technology used to safeguard the data. This paper discusses how different technology frameworks have been applied to safeguard the data and facilitate collaborative work between commercial concerns and academic institutions. The paper focuses on the distinctive requirements of e-Social Science: access to large-scale data on behaviour in society in environments that impose confidentiality constraints on access. These constraints arise from both privacy concerns and the commercial sensitivities of that data. In particular, the paper draws on the experiences of building an intercontinental Grid–INWA–from its first operation connecting Australia and Scotland to its subsequent extension to China across the Trans-Eurasia Information Network–the first large-scale research and education network for the Asia-Pacific region. This allowed commercial data to be analysed by experts that were geographically distributed across the globe. It also provided an entry point for a major Chinese commercial organization to approve use of a Grid solution in a new collaboration provided the centre of gravity of the data is retained within the jurisdiction of the data owner. We describe why, despite this approval, an embedded solution was eventually adopted. We find that ‘data sovereignty’ dominates any decision on whether and how to participate in e-Social Science collaborations and how this might impact on a Cloud based solution to this type of collaboration.
VL  - 29
UR  - http://www.sciencedirect.com/science/article/pii/S0167739X12002336
IS  - 5
ER  - 

TY  - JOUR
T1  - Exploiting Parallel R in the Cloud with SPRINT
JF  - Methods of Information in Medicine
Y1  - 2013
A1  - Piotrowski, Michal
A1  - Gary McGilvary
A1  - Sloan, Terence
A1  - Mewissen, Muriel
A1  - Ashley Lloyd
A1  - Forster, Thorsten
A1  - Mitchell, Lawrence
A1  - Ghazal, Peter
A1  - Hill, Jon
AB  - Background: Advances in DNA Microarray devices and next-generation massively parallel DNA sequencing platforms have led to an exponential growth in data availability but the arising opportunities require adequate computing resources. High Performance Computing (HPC) in the Cloud offers an affordable way of meeting this need.    Objectives: Bioconductor, a popular tool for high-throughput genomic data analysis, is distributed as add-on modules for the R statistical programming language but R has no native capabilities for exploiting multi-processor architectures. SPRINT is an R package that enables easy access to HPC for genomics researchers. This paper investigates: setting up and running SPRINT-enabled genomic analyses on Amazon’s Elastic Compute Cloud (EC2), the advantages of submitting applications to EC2 from different parts of the world and, if resource underutilization can improve application performance.    Methods: The SPRINT parallel implementations of correlation, permutation testing, partitioning around medoids and the multi-purpose papply have been benchmarked on data sets of various size on Amazon EC2. Jobs have been submitted from both the UK and Thailand to investigate monetary differences.    Results: It is possible to obtain good, scalable performance but the level of improvement is dependent upon the nature of algorithm. Resource underutilization can further improve the time to result. End-user’s location impacts on costs due to factors such as local taxation.     Conclusions: Although not designed to satisfy HPC requirements, Amazon EC2 and cloud computing in general provides an interesting alternative and provides new possibilities for smaller organisations with limited funds.
VL  - 52
IS  - 1
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  - 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  - Towards automatic detection of abnormal retinal capillaries in ultra-widefield-of-view retinal angiographic exams
T2  - Conf Proc IEEE Eng Med Biol Soc
Y1  - 2013
A1  - Zutis, K.
A1  - Trucco, E.
A1  - Hubschman, J. P.
A1  - Reed, D.
A1  - Shah, S.
A1  - van Hemert, J.
KW  - retinal imaging
AB  - Retinal capillary abnormalities include small, leaky, severely tortuous blood vessels that are associated with a variety of retinal pathologies. We present a prototype image-processing system for detecting abnormal retinal capillary regions in ultra-widefield-of-view (UWFOV) fluorescein angiography exams of the human retina. The algorithm takes as input an UWFOV FA frame and returns the candidate regions identified. An SVM classifier is trained on regions traced by expert ophthalmologists. Tests with a variety of feature sets indicate that edge features and allied properties differentiate best between normal and abnormal retinal capillary regions. Experiments with an initial set of images from patients showing branch retinal vein occlusion (BRVO) indicate promising area under the ROC curve of 0.950 and a weighted Cohen's Kappa value of 0.822.
JF  - Conf Proc IEEE Eng Med Biol Soc
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 Data Driven Science Gateway for Computational Workflows
T2  - UNICORE Summit 2012
Y1  - 2012
A1  - Grunzke, Richard
A1  - Birkenheuer, G.
A1  - Blunk, D.
A1  - Breuers, S.
A1  - Brinkmann, A.
A1  - Gesing, Sandra
A1  - Herres-Pawlis, S
A1  - Kohlbacher, O.
A1  - Krüger, J.
A1  - Kruse, M.
A1  - Müller-Pfefferkorn, R.
A1  - Schäfer, P.
A1  - Schuller, B.
A1  - Steinke, T.
A1  - Zink, A.
JF  - UNICORE Summit 2012
ER  - 

TY  - CONF
T1  - A databank, rather than statistical, model of normal ageing brain structure to indicate pathology
T2  - OHBM 2012
Y1  - 2012
A1  - Dickie, David Alexander
A1  - Dominic Job
A1  - Rodríguez, David
A1  - Shenkin, Susan
A1  - Wardlaw, Joanna
JF  - OHBM 2012
UR  - http://ww4.aievolution.com/hbm1201/index.cfm?do=abs.viewAbs&abs=5102
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  - CONF
T1  - Generic User Management for Science Gateways via Virtual Organizations
T2  - EGI Technical Forum 2012
Y1  - 2012
A1  - Schlemmer, Tobias
A1  - Grunzke, Richard
A1  - Gesing, Sandra
A1  - Krüger, Jens
A1  - Birkenheuer, Georg
A1  - Müller-Pfefferkorn, Ralph
A1  - Kohlbacher, Oliver
JF  - EGI Technical Forum 2012
ER  - 

TY  - Generic
T1  - HealthGrid Applications and Technologies Meet Science Gateways for Life Sciences
Y1  - 2012
ED  - Gesing, Sandra
ED  - Glatard, Tristan
ED  - Krüger, Jens
ED  - Delgado Olabarriaga, Silvia
ED  - Solomonides, Tony
ED  - Silverstein, J.
ED  - Montagnat, J.
ED  - Gaignard, A.
ED  - Krefting, Dagmar
PB  - IOS Press
VL  - 175
ER  - 

TY  - CONF
T1  - The MoSGrid Community - From National to International Scale
T2  - EGI Community Forum 2012
Y1  - 2012
A1  - Gesing, Sandra
A1  - Herres-Pawlis, Sonja
A1  - Birkenheuer, Georg
A1  - Brinkmann, André
A1  - Grunzke, Richard
A1  - Kacsuk, Peter
A1  - Kohlbacher, Oliver
A1  - Kozlovszky, Miklos
A1  - Krüger, Jens
A1  - Müller-Pfefferkorn, Ralph
A1  - Schäfer, Patrick
A1  - Steinke, Thomas
JF  - EGI Community Forum 2012
ER  - 

TY  - CONF
T1  - MoSGrid: Progress of Workflow driven Chemical Simulations
T2  - Grid Workflow Workshop 2011
Y1  - 2012
A1  - Birkenheuer, Georg
A1  - Blunk, Dirk
A1  - Breuers, Sebastian
A1  - Brinkmann, André
A1  - Fels, Gregor
A1  - Gesing, Sandra
A1  - Grunzke, Richard
A1  - Herres-Pawlis, Sonja
A1  - Kohlbacher, Oliver
A1  - Krüger, Jens
A1  - Packschies, Lars
A1  - Schäfer, Patrick
A1  - Schuller, B.
A1  - Schuster, Johannes
A1  - Steinke, Thomas
A1  - Szikszay Fabri, Anna
A1  - Wewior, Martin
A1  - Müller-Pfefferkorn, Ralph
A1  - Kohlbacher, Oliver
JF  - Grid Workflow Workshop 2011
PB  - CEUR Workshop Proceedings
ER  - 

TY  - CONF
T1  - A Science Gateway Getting Ready for Serving the International Molecular Simulation Community
T2  - Proceedings of Science
Y1  - 2012
A1  - Gesing, Sandra
A1  - Herres-Pawlis, Sonja
A1  - Birkenheuer, Georg
A1  - Brinkmann, André
A1  - Grunzke, Richard
A1  - Kacsuk, Peter
A1  - Kohlbacher, Oliver
A1  - Kozlovszky, Miklos
A1  - Krüger, Jens
A1  - Müller-Pfefferkorn, Ralph
A1  - Schäfer, Patrick
A1  - Steinke, Thomas
JF  - Proceedings of Science
ER  - 

TY  - JOUR
T1  - A Single Sign-On Infrastructure for Science Gateways on a Use Case for Structural Bioinformatics
JF  - Journal of Grid Computing
Y1  - 2012
A1  - Gesing, Sandra
A1  - Grunzke, Richard
A1  - Krüger, Jens
A1  - Birkenheuer, Georg
A1  - Wewior, Martin
A1  - Schäfer, Patrick
A1  - Schuller, Bernd
A1  - Schuster, Johannes
A1  - Herres-Pawlis, Sonja
A1  - Breuers, Sebastian
A1  - Balaskó, Ákos
A1  - Kozlovszky, Miklos
A1  - Fabri, AnnaSzikszay
A1  - Packschies, Lars
A1  - Kacsuk, Peter
A1  - Blunk, Dirk
A1  - Steinke, Thomas
A1  - Brinkmann, André
A1  - Fels, Gregor
A1  - Müller-Pfefferkorn, Ralph
A1  - Jäkel, René
A1  - Kohlbacher, Oliver
KW  - DCIs
KW  - Science gateway
KW  - security
KW  - Single sign-on
KW  - Structural bioinformatics
VL  - 10
UR  - http://dx.doi.org/10.1007/s10723-012-9247-y
ER  - 

TY  - JOUR
T1  - Discovering the suitability of optimisation algorithms by learning from evolved instances
JF  - Annals of Mathematics and Artificial Intelligence
Y1  - 2011
A1  - K. Smith-Miles
A1  - {van Hemert}, J. I.
KW  - problem evolving
VL  - Online Fir
UR  - http://www.springerlink.com/content/6x83q3201gg71554/
ER  - 

TY  - JOUR
T1  - An evaluation of ontology matching in geo-service applications
JF  - Geoinformatica
Y1  - 2011
A1  - Lorenzino Vaccari
A1  - Pavel Shvaiko
A1  - Juan Pane
A1  - Paolo Besana
A1  - Maurizio Marchese
ER  - 

TY  - CONF
T1  - Granular Security for a Science Gateway in Structural Bioinformatics
T2  - Proceedings of the International Workshop on Science Gateways for Life Sciences (IWSG-Life 2011)
Y1  - 2011
A1  - Gesing, Sandra
A1  - Grunzke, Richard
A1  - Balaskó, Ákos
A1  - Birkenheuer, Georg
A1  - Blunk, Dirk
A1  - Breuers, Sebastian
A1  - Brinkmann, André
A1  - Fels, Gregor
A1  - Herres-Pawlis, Sonja
A1  - Kacsuk, Peter
A1  - Kozlovszky, Miklos
A1  - Krüger, Jens
A1  - Packschies, Lars
A1  - Schäfer, Patrick
A1  - Schuller, Bernd
A1  - Schuster, Johannes
A1  - Steinke, Thomas
A1  - Szikszay Fabri, Anna
A1  - Wewior, Martin
A1  - Müller-Pfefferkorn, Ralph
A1  - Kohlbacher, Oliver
JF  - Proceedings of the International Workshop on Science Gateways for Life Sciences (IWSG-Life 2011)
PB  - CEUR Workshop Proceedings
ER  - 

TY  - CONF
T1  - A Science Gateway for Molecular Simulations
T2  - EGI User Forum 2011
Y1  - 2011
A1  - Gesing, Sandra
A1  - Kacsuk, Peter
A1  - Kozlovszky, Miklos
A1  - Birkenheuer, Georg
A1  - Blunk, Dirk
A1  - Breuers, Sebastian
A1  - Brinkmann, André
A1  - Fels, Gregor
A1  - Grunzke, Richard
A1  - Herres-Pawlis, Sonja
A1  - Krüger, Jens
A1  - Packschies, Lars
A1  - Müller-Pfefferkorn, Ralph
A1  - Schäfer, Patrick
A1  - Steinke, Thomas
A1  - Szikszay Fabri, Anna
A1  - Warzecha, Klaus
A1  - Wewior, Martin
A1  - Kohlbacher, Oliver
JF  - EGI User Forum 2011
SN  - 978 90 816927 1 7
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  - CONF
T1  - Accelerating Data-Intensive Applications: a Cloud Computing Approach Image Pattern Recognition Tasks
T2  - The Fourth International Conference on Advanced Engineering Computing and Applications in Sciences
Y1  - 2010
A1  - Han, L
A1  - Saengngam, T.
A1  - van Hemert, J.
JF  - The Fourth International Conference on Advanced Engineering Computing and Applications in Sciences
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  - Correcting for intra-experiment variation in Illumina BeadChip data is necessary to generate robust gene-expression profiles
JF  - BMC Genomics
Y1  - 2010
A1  - R. R. Kitchen
A1  - V. S. Sabine
A1  - A. H. Sims
A1  - E. J. Macaskill
A1  - L. Renshaw
A1  - J. S. Thomas
A1  - van Hemert, J. I.
A1  - J. M. Dixon
A1  - J. M. S. Bartlett
AB  - Background    Microarray technology is a popular means of producing whole genome transcriptional profiles, however high cost and scarcity of mRNA has led many studies to be conducted based on the analysis of single samples. We exploit the design of the Illumina platform, specifically multiple arrays on each chip, to evaluate intra-experiment technical variation using repeated hybridisations of universal human reference RNA (UHRR) and duplicate hybridisations of primary breast tumour samples from a clinical study.    Results    A clear batch-specific bias was detected in the measured expressions of both the UHRR and clinical samples. This bias was found to persist following standard microarray normalisation techniques. However, when mean-centering or empirical Bayes batch-correction methods (ComBat) were applied to the data, inter-batch variation in the UHRR and clinical samples were greatly reduced. Correlation between replicate UHRR samples improved by two orders of magnitude following batch-correction using ComBat (ranging from 0.9833-0.9991 to 0.9997-0.9999) and increased the consistency of the gene-lists from the duplicate clinical samples, from 11.6% in quantile normalised data to 66.4% in batch-corrected data. The use of UHRR as an inter-batch calibrator provided a small additional benefit when used in conjunction with ComBat, further increasing the agreement between the two gene-lists, up to 74.1%.    Conclusion    In the interests of practicalities and cost, these results suggest that single samples can generate reliable data, but only after careful compensation for technical bias in the experiment. We recommend that investigators appreciate the propensity for such variation in the design stages of a microarray experiment and that the use of suitable correction methods become routine during the statistical analysis of the data.
VL  - 11
UR  - http://www.biomedcentral.com/1471-2164/11/134
IS  - 134
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  - CONF
T1  - Understanding TSP Difficulty by Learning from Evolved Instances
T2  - Lecture Notes in Computer Science
Y1  - 2010
A1  - Smith-Miles, Kate
A1  - van Hemert, Jano
A1  - Lim, Xin
ED  - Blum, Christian
ED  - Battiti, Roberto
AB  - Whether the goal is performance prediction, or insights into the relationships between algorithm performance and instance characteristics, a comprehensive set of meta-data from which relationships can be learned is needed. This paper provides a methodology to determine if the meta-data is sufficient, and demonstrates the critical role played by instance generation methods. Instances of the Travelling Salesman Problem (TSP) are evolved using an evolutionary algorithm to produce distinct classes of instances that are intentionally easy or hard for certain algorithms. A comprehensive set of features is used to characterise instances of the TSP, and the impact of these features on difficulty for each algorithm is analysed. Finally, performance predictions are achieved with high accuracy on unseen instances for predicting search effort as well as identifying the algorithm likely to perform best.
JF  - Lecture Notes in Computer Science
PB  - Springer Berlin / Heidelberg
VL  - 6073
UR  - http://dx.doi.org/10.1007/978-3-642-13800-3_29
N1  - 10.1007/978-3-642-13800-3_29
ER  - 

TY  - CONF
T1  - Workflow Interoperability in a Grid Portal for Molecular Simulations
T2  - Proceedings of the International Workshop on Science Gateways (IWSG10)
Y1  - 2010
A1  - Gesing, Sandra
A1  - Marton, Istvan
A1  - Birkenheuer, Georg
A1  - Schuller, Bernd
A1  - Grunzke, Richard
A1  - Krüger, Jens
A1  - Breuers, Sebastian
A1  - Blunk, Dirk
A1  - Fels, Gregor
A1  - Packschies, Lars
A1  - Brinkmann, André
A1  - Kohlbacher, Oliver
A1  - Kozlovszky, Miklos
JF  - Proceedings of the International Workshop on Science Gateways (IWSG10)
PB  - Consorzio COMETA
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 oers 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 dicult.  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  - JOUR
T1  - Design and Optimization of Reverse-Transcription Quantitative PCR Experiments
JF  - Clin Chem
Y1  - 2009
A1  - Tichopad, Ales
A1  - Kitchen, Rob
A1  - Riedmaier, Irmgard
A1  - Becker, Christiane
A1  - Stahlberg, Anders
A1  - Kubista, Mikael
AB  - BACKGROUND: Quantitative PCR (qPCR) is a valuable technique for accurately and reliably profiling and quantifying gene expression.  Typically, samples obtained from the organism of study have to be processed via several preparative steps before qPCR. METHOD: We estimated the errors of sample withdrawal and extraction, reverse transcription (RT), and qPCR that are introduced into measurements of mRNA concentrations.  We performed hierarchically arranged experiments with 3 animals, 3 samples, 3 RT reactions, and 3 qPCRs and quantified the expression of several genes in solid tissue, blood, cell culture, and single cells. RESULTS: A nested ANOVA design was used to model the experiments, and relative and absolute errors were calculated with this model for each processing level in the hierarchical design.  We found that intersubject differences became easily confounded by sample heterogeneity for single cells and solid tissue.  In cell cultures and blood, the noise from the RT and qPCR steps contributed substantially to the overall error because the sampling noise was less pronounced. CONCLUSIONS: We recommend the use of sample replicates preferentially to any other replicates when working with solid tissue, cell cultures, and single cells, and we recommend the use of RT replicates when working with blood.  We show how an optimal sampling plan can be calculated for a limited budget.
UR  - http://www.clinchem.org/cgi/content/abstract/clinchem.2009.126201v1
ER  - 

TY  - Generic
T1  - A Methodology for Mobile Network Security Risk Management
T2  - Sixth International Conference on Information Technology: New Generations (ITNG '09)
Y1  - 2009
A1  - Mahdi Seify
A1  - Shahriar Bijani
JF  - Sixth International Conference on Information Technology: New Generations (ITNG '09)
PB  - IEEE Computer Society
ER  - 

TY  - JOUR
T1  - An Open Grid Services Architecture Primer
JF  - Computer
Y1  - 2009
A1  - Grimshaw, Andrew
A1  - Morgan, Mark
A1  - Merrill, Duane
A1  - Kishimoto, Hiro
A1  - Savva, Andreas
A1  - Snelling, David
A1  - Smith, Chris
A1  - Dave Berry
PB  - IEEE Computer Society Press
CY  - Los Alamitos, CA, USA
VL  - 42
ER  - 

TY  - JOUR
T1  - Simultaneous alignment of short reads against multiple genomes
JF  - Genome Biol
Y1  - 2009
A1  - Schneeberger, Korbinian
A1  - Hagmann, Jörg
A1  - Ossowski, Stephan
A1  - Warthmann, Norman
A1  - Gesing, Sandra
A1  - Kohlbacher, Oliver
A1  - Weigel, Detlef
VL  - 10
UR  - http://www.biomedsearch.com/nih/Simultaneous-alignment-short-reads-against/19761611.html
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 4: Training Infrastructure
JF  - Distributed Systems Online
Y1  - 2008
A1  - Fergusson, D.
A1  - Barbera, R.
A1  - Giorgio, E.
A1  - Fargetta, M.
A1  - Sipos, G.
A1  - Romano, D.
A1  - Atkinson, M.
A1  - Vander Meer, E.
AB  - In the first article of this series (see http://doi.ieeecomputersociety.org/10.1109/MDSO.2008.16), we identified the need for teaching environments that provide infrastructure to support education and training in distributed computing. Training infrastructure, or t-infrastructure, is analogous to the teaching laboratory in biology and is a vital tool for educators and students. In practice, t-infrastructure includes the computing equipment, digital communications, software, data, and support staff necessary to teach a course. The International Summer Schools in Grid Computing (ISSGC) series and the first International Winter School on Grid Computing (IWSGC 08) used the Grid INFN Laboratory of Dissemination Activities (GILDA) infrastructure so students could gain hands-on experience with middleware. Here, we describe GILDA, related summer and winter school experiences, multimiddleware integration, t-infrastructure, and academic courses, concluding with an analysis and recommendations.
PB  - IEEE Computer Society
VL  - 9
UR  - http://ieeexplore.ieee.org/stamp/stamp.jsp?tp=&arnumber=4752926
IS  - 10
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  - 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  - CONF
T1  - Data Integration in eHealth: A Domain/Disease Specific Roadmap
T2  - Studies in Health Technology and Informatics
Y1  - 2007
A1  - Ure, J.
A1  - Proctor, R.
A1  - Martone, M.
A1  - Porteous, D.
A1  - Lloyd, S.
A1  - Lawrie, S.
A1  - Job, D.
A1  - Baldock, R.
A1  - Philp, A.
A1  - Liewald, D.
A1  - Rakebrand, F.
A1  - Blaikie, A.
A1  - McKay, C.
A1  - Anderson, S.
A1  - Ainsworth, J.
A1  - van Hemert, J.
A1  - Blanquer, I.
A1  - Sinno
ED  - N. Jacq
ED  - Y. Legr{\'e}
ED  - H. Muller
ED  - I. Blanquer
ED  - V. Breton
ED  - D. Hausser
ED  - V. Hern{\'a}ndez
ED  - T. Solomonides
ED  - M. Hofman-Apitius
KW  - e-Science
AB  - The paper documents a series of data integration workshops held in 2006 at the UK National e-Science Centre, summarizing a range of the problem/solution scenarios in multi-site and multi-scale data integration with six HealthGrid projects using schizophrenia as a domain-specific test case. It outlines   emerging strategies, recommendations and objectives for collaboration on shared ontology-building and harmonization of data for multi-site trials in this domain.
JF  - Studies in Health Technology and Informatics
PB  - IOPress
VL  - 126
SN  - 978-1-58603-738-3
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  - JOUR
T1  - MAPFS-DAI, an extension of OGSA-DAI based on a parallel file system
JF  - Future Generation Computer Systems
Y1  - 2007
A1  - Sanchez, A.
A1  - Perez, M. S.
A1  - Karasavvas, K.
A1  - Herrero, P.
A1  - Perez, A.
VL  - 23
ER  - 

TY  - JOUR
T1  - Mining co-regulated gene profiles for the detection of functional associations in gene expression data
JF  - Bioinformatics
Y1  - 2007
A1  - Gyenesei, Attila
A1  - Wagner, Ulrich
A1  - Barkow-Oesterreicher, Simon
A1  - Stolte, Etzard
A1  - Schlapbach, Ralph
VL  - 23
ER  - 

TY  - CONF
T1  - OGSA-DAI 3.0 - The What's and Whys
T2  - UK e-Science All Hands Meeting
Y1  - 2007
A1  - Antonioletti, M.
A1  - Hong, N. P. Chue
A1  - Hume, A. C.
A1  - Jackson, M.
A1  - Karasavvas, K.
A1  - Krause, A.
A1  - Schopf, J. M.
A1  - Atkinson, M. P.
A1  - Dobrzelecki, B.
A1  - Illingworth, M.
A1  - McDonnell, N.
A1  - Parsons, M.
A1  - Theocharopoulous, E.
JF  - UK e-Science All Hands Meeting
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  - Generic
T1  - Special Issue: Selected Papers from the 2004 U.K. e-Science All Hands Meeting
T2  - All Hands Meeting 2004
Y1  - 2007
A1  - Walker, D. W.
A1  - Atkinson, M. P.
A1  - Sommerville, I.
ED  - Walker, D. W.
ED  - Atkinson, M. P.
ED  - Sommerville, I.
JF  - All Hands Meeting 2004
T3  - Concurrency and Computation: Practice and Experience
PB  - John Wiley & Sons Ltd
CY  - Nottingham, UK
VL  - 19
ER  - 

TY  - CONF
T1  - Study of User Priorities for e-Infrastructure for e-Research (SUPER)
T2  - Proceedings of the UK e-Science All Hands Meeting
Y1  - 2007
A1  - Newhouse, S.
A1  - Schopf, J. M.
A1  - Richards, A.
A1  - Atkinson, M. P.
JF  - Proceedings of the UK e-Science All Hands Meeting
ER  - 

TY  - CONF
T1  - Towards a Grid-Enabled Simulation Framework for Nano-CMOS Electronics
T2  - 3rd IEEE International Conference on eScience and Grid Computing
Y1  - 2007
A1  - Liangxiu Han
A1  - Asen Asenov
A1  - Dave Berry
A1  - Campbell Millar
A1  - Gareth Roy
A1  - Scott Roy
A1  - Richard Sinnott
A1  - Gordon Stewart
AB  - The electronics design industry is facing major challenges as transistors continue to decrease in size.  The next generation of devices will be so small that the position of individual atoms will affect their behaviour.  This will cause the transistors on a chip to have highly variable characteristics, which in turn will impact  circuit and system design tools. The EPSRC project “Meeting the Design Challenges of Nano-CMOS  Electronics” (Nano-CMOS) has been funded to explore this area. In this paper, we describe the  distributed data-management and computing framework under development within Nano-CMOS. A  key aspect of this framework is the need for robust and reliable security mechanisms that support distributed  electronics design groups who wish to collaborate by sharing designs, simulations, workflows, datasets and  computation resources. This paper presents the system design, and an early prototype of the project which hasbeen useful in helping us to understand the benefits of such a grid infrastructure. In particular, we also present two typical use cases: user authentication, and execution of large-scale device simulations.
JF  - 3rd IEEE International Conference on eScience and Grid Computing
PB  - IEEE Computer Society
CY  - Bangalore, India
ER  - 

TY  - CONF
T1  - Grid Enabling your Data Resources with OGSA-DAI
T2  - Workshop on State-of-the-Art in Scientific and Parallel Computing
Y1  - 2006
A1  - Antonioletti, M.
A1  - Atkinson, M.
A1  - Hong, N. Chue
A1  - Dobrzelecki, B.
A1  - Hume, A.
A1  - Jackson, M.
A1  - Karasavvas, K.
A1  - Krause, A.
A1  - Sugden, T.
A1  - Theocharopoulos, E.
JF  - Workshop on State-of-the-Art in Scientific and Parallel Computing
ER  - 

TY  - CONF
T1  - Grid Infrastructures for Secure Access to and Use of Bioinformatics Data: Experiences from the BRIDGES Project
T2  - Proceedings of the First International Conference on Availability, Reliability and Security, ARES
Y1  - 2006
A1  - Richard O. Sinnott
A1  - Micha Bayer
A1  - A. J. Stell
A1  - Jos Koetsier
JF  - Proceedings of the First International Conference on Availability, Reliability and Security, ARES
T3  - Proceedings of the The First International Conference on Availability, Reliability and Security
CY  - Vienna, Austria
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  - CONF
T1  - Profiling OGSA-DAI Performance for Common Use Patterns
T2  - UK e-Science All Hands Meeting
Y1  - 2006
A1  - Dobrzelecki, B.
A1  - Antonioletti, M.
A1  - Schopf, J. M.
A1  - Hume, A. C.
A1  - Atkinson, M.
A1  - Hong, N. P. Chue
A1  - Jackson, M.
A1  - Karasavvas, K.
A1  - Krause, A.
A1  - Parsons, M.
A1  - Sugden, T.
A1  - Theocharopoulos, E.
JF  - UK e-Science All Hands Meeting
ER  - 

TY  - CONF
T1  - A Shibboleth-Protected Privilege Management Infrastructure for e-Science Education
T2  - Sixth IEEE International Symposium on Cluster Computing and the Grid (CCGrid 2006
Y1  - 2006
A1  - J. Watt
A1  - Oluwafemi Ajayi
A1  - J. Jiang
A1  - Jos Koetsier
A1  - Richard O. Sinnott
KW  - security
JF  - Sixth IEEE International Symposium on Cluster Computing and the Grid (CCGrid 2006
PB  - IEEE Computer Society
CY  - Singapore
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  - CONF
T1  - Introduction to OGSA-DAI Services
T2  - Scientific Applications of Grid Computing
Y1  - 2005
A1  - Karasavvas, K.
A1  - Antonioletti, M.
A1  - Atkinson, M.
A1  - Hong, N. C.
A1  - Sugden, T.
A1  - Hume, A.
A1  - Jackson, M.
A1  - Krause, A.
A1  - Palansuriya, C.
JF  - Scientific Applications of Grid Computing
VL  - 3458
SN  - 978-3-540-25810-0
ER  - 

TY  - CONF
T1  - A New Architecture for OGSA-DAI
T2  - UK e-Science All Hands Meeting
Y1  - 2005
A1  - Atkinson, M.
A1  - Karasavvas, K.
A1  - Antonioletti, M.
A1  - Baxter, R.
A1  - Borley, A.
A1  - Hong, N. C.
A1  - Hume, A.
A1  - Jackson, M.
A1  - Krause, A.
A1  - Laws, S.
A1  - Paton, N.
A1  - Schopf, J.
A1  - Sugden, T.
A1  - Tourlas, K.
A1  - Watson, P.
JF  - UK e-Science All Hands Meeting
ER  - 

TY  - CONF
T1  - OGSA-DAI Status and Benchmarks
T2  - All Hands Meeting 2005
Y1  - 2005
A1  - Antonioletti, Mario
A1  - Malcolm Atkinson
A1  - Rob Baxter
A1  - Andrew Borle
A1  - Hong, Neil P. Chue
A1  - Patrick Dantressangle
A1  - Hume, Alastair C.
A1  - Mike Jackson
A1  - Krause, Amy
A1  - Laws, Simon
A1  - Parsons, Mark
A1  - Paton, Norman W.
A1  - Jennifer M. Schopf
A1  - Tom Sugden
A1  - Watson, Paul
AB  - This paper presents a status report on some of the highlights that have taken place within the OGSADAI project since the last AHM. A description of Release 6.0 functionality and details of the forthcoming release, due in September 2005, is given. Future directions for this project are discussed. This paper also describes initial results of work being done to systematically benchmark recent OGSADAI releases. The OGSA-DAI software distribution, and more information about the project, is available from the project website at www.ogsadai.org.uk.
JF  - All Hands Meeting 2005
CY  - Nottingham, UK
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  - Generic
T1  - Development of a Grid Infrastructure for Functional Genomics
T2  - Life Science Grid Conference (LSGrid 2004)
Y1  - 2004
A1  - Sinnott, R. O.
A1  - Bayer, M.
A1  - Houghton, D.
A1  - D. Berry
A1  - Ferrier, M.
JF  - Life Science Grid Conference (LSGrid 2004)
T3  - LNCS
PB  - Springer Verlag
CY  - Kanazawa, Japan
ER  - 

TY  - CONF
T1  - Dynamic Routing Problems with Fruitful Regions: Models and Evolutionary Computation
T2  - LNCS
Y1  - 2004
A1  - van Hemert, J. I.
A1  - la Poutré, J. A.
ED  - Xin Yao
ED  - Edmund Burke
ED  - Jose A. Lozano
ED  - Jim Smith
ED  - Juan J. Merelo-Guerv\'os
ED  - John A. Bullinaria
ED  - Jonathan Rowe
ED  - Peter Ti\v{n}o Ata Kab\'an
ED  - Hans-Paul Schwefel
KW  - dynamic problems
KW  - evolutionary computation
KW  - vehicle routing
AB  - We introduce the concept of fruitful regions in a dynamic routing context: regions that have a high potential of generating loads to be transported. The objective is to maximise the number of loads transported, while keeping to capacity and time constraints. Loads arrive while the problem is being solved, which makes it a real-time routing problem. The solver is a self-adaptive evolutionary algorithm that ensures feasible solutions at all times. We investigate under what conditions the exploration of fruitful regions improves the effectiveness of the evolutionary algorithm.
JF  - LNCS
PB  - Springer-Verlag
CY  - Birmingham, UK
VL  - 3242
SN  - 3-540-23092-0
ER  - 

TY  - Generic
T1  - Grid Services Supporting the Usage of Secure Federated, Distributed Biomedical Data
T2  - All Hands Meeting 2004
Y1  - 2004
A1  - Richard Sinnott
A1  - Malcolm Atkinson
A1  - Micha Bayer
A1  - Dave Berry
A1  - Anna Dominiczak
A1  - Magnus Ferrier
A1  - David Gilbert
A1  - Neil Hanlon
A1  - Derek Houghton
A1  - Hunt, Ela
A1  - David White
AB  - The BRIDGES project is a UK e-Science project that provides grid based support for biomedical research into the genetics of hypertension – the Cardiovascular Functional Genomics Project (CFG). Its main goal is to provide an effective environment for CFG, and biomedical research in general, including access to integrated data, analysis and visualization, with appropriate authorisation and privacy, as well as grid based computational tools and resources. It also aims to provide an improved understanding of the requirements of academic biomedical research virtual organizations and to evaluate the utility of existing data federation tools.
JF  - All Hands Meeting 2004
CY  - Nottingham, UK
UR  - http://www.allhands.org.uk/2004/proceedings/papers/87.pdf
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  - Phase transition properties of clustered travelling salesman problem instances generated with evolutionary computation
T2  - LNCS
Y1  - 2004
A1  - van Hemert, J. I.
A1  - Urquhart, N. B.
ED  - Xin Yao
ED  - Edmund Burke
ED  - Jose A. Lozano
ED  - Jim Smith
ED  - Juan J. Merelo-Guerv\'os
ED  - John A. Bullinaria
ED  - Jonathan Rowe
ED  - Peter Ti\v{n}o Ata Kab\'an
ED  - Hans-Paul Schwefel
KW  - evolutionary computation
KW  - problem evolving
KW  - travelling salesman
AB  - This paper introduces a generator that creates problem instances for the Euclidean symmetric travelling salesman problem. To fit real world problems, we look at maps consisting of clustered nodes. Uniform random sampling methods do not result in maps where the nodes are spread out to form identifiable clusters. To improve upon this, we propose an evolutionary algorithm that uses the layout of nodes on a map as its genotype. By optimising the spread until a set of constraints is satisfied, we are able to produce better clustered maps, in a more robust way. When varying the number of clusters in these maps and, when solving the Euclidean symmetric travelling salesman person using Chained Lin-Kernighan, we observe a phase transition in the form of an easy-hard-easy pattern.
JF  - LNCS
PB  - Springer-Verlag
CY  - Birmingham, UK
VL  - 3242
SN  - 3-540-23092-0
UR  - http://www.vanhemert.co.uk/files/clustered-phase-transition-tsp.tar.gz
ER  - 

TY  - CONF
T1  - A Study into Ant Colony Optimization, Evolutionary Computation and Constraint Programming on Binary Constraint Satisfaction Problems
T2  - Springer Lecture Notes on Computer Science
Y1  - 2004
A1  - van Hemert, J. I.
A1  - Solnon, C.
ED  - J. Gottlieb
ED  - G. Raidl
KW  - ant colony optimisation
KW  - constraint programming
KW  - constraint satisfaction
KW  - evolutionary computation
AB  - We compare two heuristic approaches, evolutionary computation and ant colony optimisation, and a complete tree-search approach, constraint programming, for solving binary constraint satisfaction problems. We experimentally show that, if evolutionary computation is far from being able to compete with the two other approaches, ant colony optimisation nearly always succeeds in finding a solution, so that it can actually compete with constraint programming.  The resampling ratio is used to provide insight into heuristic algorithms performances. Regarding efficiency, we show that if constraint programming is the fastest when instances have a low number of variables, ant colony optimisation becomes faster when increasing the number of variables.
JF  - Springer Lecture Notes on Computer Science
PB  - Springer-Verlag, Berlin
SN  - 3-540-21367-8
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  - JOUR
T1  - The DWMM network traffic model
JF  - Journal of Communication
Y1  - 2003
A1  - Cong Suo
A1  - Liangxiu Han
VL  - 24
IS  - 5
ER  - 

TY  - CONF
T1  - Experiences of Designing and Implementing Grid Database Services in the OGSA-DAI project
T2  - Global Grid Forum Workshop on Designing and Building Grid Services/GGF9
Y1  - 2003
A1  - Antonioletti, Mario
A1  - Neil Chue Hong
A1  - Ally Hume
A1  - Mike Jackson
A1  - Krause, Amy
A1  - Jeremy Nowell
A1  - Charaka Palansuriya
A1  - Tom Sugden
A1  - Martin Westhead
AB  - This paper describes the experiences of the OGSA-DAI team in designing and building a database access layer using the OGSI and the emerging DAIS GGF recommendations. This middleware is designed for enabling other UK e-Science projects that require database access and providing the basic primitives for higher-level services such as Distributed Query Processing. OGSA-DAI also intends to produce one of the required reference implementations of the DAIS specification once this becomes a proposed recommendation and, until then, scope out their ideas, provide feedback as well as directly contributing to the GGF working group. This paper enumerates the issues that have arisen in tracking the DAIS and OGSI specifications whilst developing a software distribution using the Grid services model; trying to serve the needs of the various target communities; and using the Globus Toolkit OGSI core distribution. The OGSA-DAI software distribution and more details are available from the project web site at http://www.ogsadai.org.uk/.
JF  - Global Grid Forum Workshop on Designing and Building Grid Services/GGF9
CY  - Chicago, USA
ER  - 

TY  - RPRT
T1  - Grid Database Access and Integration: Requirements and Functionalities
Y1  - 2003
A1  - Atkinson, M. P.
A1  - Dialani, V.
A1  - Guy, L.
A1  - Narang, I.
A1  - Paton, N. W.
A1  - Pearson, D.
A1  - Storey, T.
A1  - Watson, P.
AB  - This document is intended to provide the context for developing Grid data service standard recommendations within the Global Grid Forum. It defines the generic requirements for accessing and integrating persistent structured and semi-structured data. In addition, it defines the generic functionalities which a Grid data service needs to provide in supporting discovery of and controlled access to data, in performing data manipulation operations, and in virtualising data resources. The document also defines the scope of Grid data service standard recommendations which are presented in a separate document.
JF  - Global Grid Forum
ER  - 

TY  - CONF
T1  - Measuring the Searched Space to Guide Efficiency: The Principle and Evidence on Constraint Satisfaction
T2  - Springer Lecture Notes on Computer Science
Y1  - 2002
A1  - van Hemert, J. I.
A1  - Bäck, T.
ED  - J. J. Merelo
ED  - A. Panagiotis
ED  - H.-G. Beyer
ED  - Jos{\'e}-Luis Fern{\'a}ndez-Villaca{\~n}as
ED  - Hans-Paul Schwefel
KW  - constraint satisfaction
KW  - resampling ratio
AB  - In this paper we present a new tool to measure the efficiency of evolutionary algorithms by storing the whole searched space of a run, a process whereby we gain insight into the number of distinct points in the state space an algorithm has visited as opposed to the number of function evaluations done within the run. This investigation demonstrates a certain inefficiency of the classical mutation operator with mutation-rate 1/l, where l is the dimension of the state space. Furthermore we present a model for predicting this inefficiency and verify it empirically using the new tool on binary constraint satisfaction problems.
JF  - Springer Lecture Notes on Computer Science
PB  - Springer-Verlag, Berlin
SN  - 3-540-44139-5
ER  - 

TY  - JOUR
T1  - The characterizing network traffic based on the wavelet technique
JF  - Journal of Mini-Micro Computer System
Y1  - 2001
A1  - Liangxiu Han
A1  - Cong Suo
VL  - 22
IS  - 9
ER  - 

TY  - CONF
T1  - An Engineering Approach to Evolutionary Art
T2  - Proceedings of the Genetic and Evolutionary Computation Conference (GECCO-2001)
Y1  - 2001
A1  - van Hemert, J. I.
A1  - Jansen, M. L. M.
ED  - Lee Spector
ED  - Erik D. Goodman
ED  - Annie Wu
ED  - W. B. Langdon
ED  - Hans-Michael Voigt
ED  - Mitsuo Gen
ED  - Sandip Sen
ED  - Marco Dorigo
ED  - Shahram Pezeshk
ED  - Max H. Garzon
ED  - Edmund Burke
KW  - evolutionary art
AB  - We present a general system that evolves art on the Internet. The system runs on a server which enables it to collect information about its usage world wide; its core uses operators and representations from genetic program-ming. We show two types of art that can be evolved using this general system.
JF  - Proceedings of the Genetic and Evolutionary Computation Conference (GECCO-2001)
PB  - Morgan Kaufmann Publishers, San Francisco
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  - CONF
T1  - Population dynamics and emerging features in AEGIS
T2  - Proceedings of the Genetic and Evolutionary Computation Conference
Y1  - 1999
A1  - Eiben, A. E.
A1  - Elia, D.
A1  - van Hemert, J. I.
ED  - W. Banzhaf
ED  - J. Daida
ED  - Eiben, A. E.
ED  - M. H. Garzon
ED  - V. Honavar
ED  - M. Jakiela
ED  - R. E. Smith
KW  - dynamic problems
AB  - We describe an empirical investigation within an artificial world, aegis, where a population of animals and plants is evolving. We compare different system setups in search of an `ideal' world that allows a constantly high number of inhabitants for a long period of time. We observe that high responsiveness at individual level (speed of movement) or population level (high fertility) are `ideal'.  Furthermore, we investigate the emergence of the so-called mental features of animals determining their social, consumptional and aggressive behaviour. The tests show that being socially oriented is generally advantageous, while agressive behaviour only emerges under specific circumstances.
JF  - Proceedings of the Genetic and Evolutionary Computation Conference
PB  - Morgan Kaufmann Publishers, San Francisco
ER  - 

TY  - CONF
T1  - Extended abstract: Solving Binary Constraint Satisfaction Problems using Evolutionary Algorithms with an Adaptive Fitness Function
T2  - Proceedings of the Xth Netherlands/Belgium Conference on Artificial Intelligence (NAIC'98)
Y1  - 1998
A1  - Eiben, A. E.
A1  - van Hemert, J. I.
A1  - Marchiori, E.
A1  - Steenbeek, A. G.
ED  - la Poutré, J. A.
ED  - van den Herik, J.
KW  - constraint satisfaction
JF  - Proceedings of the Xth Netherlands/Belgium Conference on Artificial Intelligence (NAIC'98)
PB  - BNVKI, Dutch and the Belgian AI Association
N1  - Abstract of \cite{EHMS98}
ER  - 

TY  - CONF
T1  - Solving Binary Constraint Satisfaction Problems using Evolutionary Algorithms with an Adaptive Fitness Function
T2  - Springer Lecture Notes on Computer Science
Y1  - 1998
A1  - Eiben, A. E.
A1  - van Hemert, J. I.
A1  - Marchiori, E.
A1  - Steenbeek, A. G.
ED  - Eiben, A. E.
ED  - Th. B{\"a}ck
ED  - M. Schoenauer
ED  - H.-P. Schwefel
KW  - constraint satisfaction
AB  - This paper presents a comparative study of Evolutionary Algorithms (EAs) for Constraint Satisfaction Problems (CSPs). We focus on EAs where fitness is based on penalization of constraint violations and the penalties are adapted during the execution. Three different EAs based on this approach are implemented. For highly connected constraint networks, the results provide further empirical support to the theoretical prediction of the phase transition in binary CSPs.
JF  - Springer Lecture Notes on Computer Science
PB  - Springer-Verlag, Berlin
ER  -