TY - CONF T1 - Applying selectively parallel IO compression to parallel storage systems T2 - Euro-Par Y1 - 2014 A1 - Rosa Filgueira A1 - Malcolm Atkinson A1 - Yusuke Tanimura A1 - Isao Kojima JF - Euro-Par ER - TY - CONF T1 - FAST: Flexible Automated Syncrhonization Transfer tool T2 - Proceedings of the Sixth International Workshop on Data-Intensive Distributed Computing Date Y1 - 2014 A1 - Rosa Filgueira A1 - Iraklis Klampanos A1 - Yusuke Tanimura A1 - Malcolm Atkinson. JF - Proceedings of the Sixth International Workshop on Data-Intensive Distributed Computing Date PB - ACM CY - New York, NY, USA 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 - 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 - CONF T1 - MPI collective I/O based on advanced reservations to obtain performance guarantees from shared storage systems T2 - CLUSTER Y1 - 2013 A1 - Yusuke Tanimura A1 - Rosa Filgueira A1 - Isao Kojima A1 - Malcolm P. Atkinson JF - CLUSTER 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 - CONF T1 - User-friendly workflows in quantum chemistry T2 - IWSG 2013 Y1 - 2013 A1 - Herres-Pawlis, Sonja A1 - Balaskó, Ákos A1 - Birkenheuer, Georg A1 - Brinkmann, André A1 - Gesing, Sandra A1 - Grunzke, Richard A1 - Hoffmann, Alexander A1 - Kacsuk, Peter A1 - Krüger, Jens A1 - Packschies, Lars A1 - Terstyansky, Gabor A1 - Weingarten, Noam JF - IWSG 2013 PB - CEUR Workshop Proceedings CY - Zurich, Switzerland UR - http://ceur-ws.org/Vol-993/paper14.pdf ER - TY - CONF T1 - Abstract: Reservation-Based I/O Performance Guarantee for MPI-IO Applications Using Shared Storage Systems T2 - SC Companion Y1 - 2012 A1 - Yusuke Tanimura A1 - Rosa Filgueira A1 - Isao Kojima A1 - Malcolm P. Atkinson JF - SC Companion ER - TY - JOUR T1 - Generating web-based user interfaces for computational science JF - Concurrency and Computation: Practice and Experience Y1 - 2011 A1 - van Hemert, J. A1 - Koetsier, J. A1 - Torterolo, L. A1 - Porro, I. A1 - Melato, M. A1 - Barbera, R. AB - Scientific gateways in the form of web portals are becoming the popular approach to share knowledge and resources around a topic in a community of researchers. Unfortunately, the development of web portals is expensive and requires specialists skills. Commercial and more generic web portals have a much larger user base and can afford this kind of development. Here we present two solutions that address this problem in the area of portals for scientific computing; both take the same approach. The whole process of designing, delivering and maintaining a portal can be made more cost-effective by generating a portal from a description rather than programming in the traditional sense. We show four successful use cases to show how this process works and the results it can deliver. PB - Wiley VL - 23 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 - Generic T1 - Federated Enactment of Workflow Patterns T2 - Lecture Notes in Computer Science Y1 - 2010 A1 - Yaikhom, Gagarine A1 - Liew, Chee A1 - Liangxiu Han A1 - van Hemert, Jano A1 - Malcolm Atkinson A1 - Krause, Amy ED - D’Ambra, Pasqua ED - Guarracino, Mario ED - Talia, Domenico AB - In this paper we address two research questions concerning workflows: 1) how do we abstract and catalogue recurring workflow patterns?; and 2) how do we facilitate optimisation of the mapping from workflow patterns to actual resources at runtime? Our aim here is to explore techniques that are applicable to large-scale workflow compositions, where the resources could change dynamically during the lifetime of an application. We achieve this by introducing a registry-based mechanism where pattern abstractions are catalogued and stored. In conjunction with an enactment engine, which communicates with this registry, concrete computational implementations and resources are assigned to these patterns, conditional to the execution parameters. Using a data mining application from the life sciences, we demonstrate this new approach. JF - Lecture Notes in Computer Science PB - Springer Berlin / Heidelberg VL - 6271 UR - http://dx.doi.org/10.1007/978-3-642-15277-1_31 N1 - 10.1007/978-3-642-15277-1_31 ER - TY - JOUR T1 - Integrating distributed data sources with OGSA--DAI DQP and Views JF - Philosophical Transactions A Y1 - 2010 A1 - Dobrzelecki, B. A1 - Krause, A. A1 - Hume, A. C. A1 - Grant, A. A1 - Antonioletti, M. A1 - Alemu, T. Y. A1 - Atkinson, M. A1 - Jackson, M. A1 - Theocharopoulos, E. AB - OGSA-DAI (Open Grid Services Architecture Data Access and Integration) is a framework for building distributed data access and integration systems. Until recently, it lacked the built-in functionality that would allow easy creation of federations of distributed data sources. The latest release of the OGSA-DAI framework introduced the OGSA-DAI DQP (Distributed Query Processing) resource. The new resource encapsulates a distributed query processor, that is able to orchestrate distributed data sources when answering declarative user queries. The query processor has many extensibility points, making it easy to customize. We have also introduced a new OGSA-DAI Views resource that provides a flexible method for defining views over relational data. The interoperability of the two new resources, together with the flexibility of the OGSA-DAI framework, allows the building of highly customized data integration solutions. VL - 368 ER - TY - CHAP T1 - Molecular Orbital Calculations of Inorganic Compounds T2 - Inorganic Experiments Y1 - 2010 A1 - C. A. Morrison A1 - N. Robertson A1 - Turner, A. A1 - van Hemert, J. A1 - Koetsier, J. ED - J. Derek Woollins JF - Inorganic Experiments PB - Wiley-VCH SN - 978-3527292530 ER - TY - JOUR T1 - Quality control for quantitative PCR based on amplification compatibility test JF - Methods Y1 - 2010 A1 - Tichopad, Ales A1 - Tzachi Bar A1 - Ladislav Pecen A1 - Robert R. Kitchen A1 - Kubista, Mikael A1 - Michael W. Pfaffl AB - Quantitative qPCR is a routinely used method for the accurate quantification of nucleic acids. Yet it may generate erroneous results if the amplification process is obscured by inhibition or generation of aberrant side-products such as primer dimers. Several methods have been established to control for pre-processing performance that rely on the introduction of a co-amplified reference sequence, however there is currently no method to allow for reliable control of the amplification process without directly modifying the sample mix. Herein we present a statistical approach based on multivariate analysis of the amplification response data generated in real-time. The amplification trajectory in its most resolved and dynamic phase is fitted with a suitable model. Two parameters of this model, related to amplification efficiency, are then used for calculation of the Z-score statistics. Each studied sample is compared to a predefined reference set of reactions, typically calibration reactions. A probabilistic decision for each individual Z-score is then used to identify the majority of inhibited reactions in our experiments. We compare this approach to univariate methods using only the sample specific amplification efficiency as reporter of the compatibility. We demonstrate improved identification performance using the multivariate approach compared to the univariate approach. Finally we stress that the performance of the amplification compatibility test as a quality control procedure depends on the quality of the reference set. PB - Elsevier VL - 50 UR - http://www.sciencedirect.com/science?_ob=ArticleURL&_udi=B6WN5-4Y88DBN-3&_user=10&_coverDate=04%2F30%2F2010&_alid=1247745718&_rdoc=1&_fmt=high&_orig=search&_cdi=6953&_sort=r&_docanchor=&view=c&_ct=2&_acct=C000050221&_version=1&_urlVersion=0&_userid=10&md5 IS - 4 ER - TY - JOUR T1 - Statistical aspects of quantitative real-time PCR experiment design JF - Methods Y1 - 2010 A1 - Robert R. Kitchen A1 - Kubista, Mikael A1 - Tichopad, Ales KW - Error propagation KW - Experiment design KW - Gene expression KW - Nested analysis of variance KW - powerNest KW - Prospective power analysis KW - qPCR KW - Real-time PCR KW - Sampling plan KW - Statistical power AB - Experiments using quantitative real-time PCR to test hypotheses are limited by technical and biological variability; we seek to minimise sources of confounding variability through optimum use of biological and technical replicates. The quality of an experiment design is commonly assessed by calculating its prospective power. Such calculations rely on knowledge of the expected variances of the measurements of each group of samples and the magnitude of the treatment effect; the estimation of which is often uninformed and unreliable. Here we introduce a method that exploits a small pilot study to estimate the biological and technical variances in order to improve the design of a subsequent large experiment. We measure the variance contributions at several ‘levels’ of the experiment design and provide a means of using this information to predict both the total variance and the prospective power of the assay. A validation of the method is provided through a variance analysis of representative genes in several bovine tissue-types. We also discuss the effect of normalisation to a reference gene in terms of the measured variance components of the gene of interest. Finally, we describe a software implementation of these methods, powerNest, that gives the user the opportunity to input data from a pilot study and interactively modify the design of the assay. The software automatically calculates expected variances, statistical power, and optimal design of the larger experiment. powerNest enables the researcher to minimise the total confounding variance and maximise prospective power for a specified maximum cost for the large study. PB - Elsevier VL - 50 UR - http://www.sciencedirect.com/science?_ob=GatewayURL&_method=citationSearch&_uoikey=B6WN5-4Y88DBN-1&_origin=SDEMFRHTML&_version=1&md5=7bb0b5b797d6e1f7c5c2df478fc88e5a IS - 4 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 - CHAP T1 - Exploiting Fruitful Regions in Dynamic Routing using Evolutionary Computation T2 - Studies in Computational Intelligence Y1 - 2009 A1 - van Hemert, J. I. A1 - la Poutré, J. A. ED - Pereira Babtista, F. ED - Tavares, J. JF - Studies in Computational Intelligence PB - Springer VL - 161 SN - 978-3-540-85151-6 N1 - Awaiting publication (due October 2008) ER - TY - CONF T1 - Rapid chemistry portals through engaging researchers T2 - Fifth IEEE International Conference on e-Science Y1 - 2009 A1 - Koetsier, J. A1 - Turner, A. A1 - Richardson, P. A1 - van Hemert, J. I. ED - Trefethen, A ED - De Roure, D AB - In this study, we apply a methodology for rapid development of portlets for scientific computing to the domain of computational chemistry. We report results in terms of the portals delivered, the changes made to our methodology and the experience gained in terms of interaction with domain-specialists. Our major contributions are: several web portals for teaching and research in computational chemistry; a successful transition to having our development tool used by the domain specialist as opposed by us, the developers; and an updated version of our methodology and technology for rapid development of portlets for computational science, which is free for anyone to pick up and use. JF - Fifth IEEE International Conference on e-Science CY - Oxford, UK ER - TY - CONF T1 - Using Simulation for Decision Support: Lessons Learned from FireGrid T2 - Proceedings of the 6th International Conference on Information Systems for Crisis Response and Management (ISCRAM 2009) Y1 - 2009 A1 - Gerhard Wickler A1 - George Beckett A1 - Liangxiu Han A1 - Sung Han Koo A1 - Stephen Potter A1 - Gavin Pringle A1 - Austin Tate ED - J. Landgren, U. Nulden ED - B. Van de Walle JF - Proceedings of the 6th International Conference on Information Systems for Crisis Response and Management (ISCRAM 2009) CY - Gothenburg, Sweden ER - TY - CONF T1 - An Architecture for an Integrated Fire Emergency Response System for the Built Environment T2 - 9th Symposium of the International Association for Fire Safety Science (IAFSS) Y1 - 2008 A1 - Rochan Upadhyay A1 - Galvin Pringle A1 - George Beckett A1 - Stephen Potter A1 - Liangxiu Han A1 - Stephen Welch A1 - Asif Usmani A1 - Jose Torero KW - emergency response system KW - FireGrid KW - system architecture KW - technology integration AB - FireGrid is a modern concept that aims to leverage a number of modern technologies to aid fire emergency response. In this paper we provide a brief introduction to the FireGrid project. A number of different technologies such as wireless sensor networks, grid-enabled High Performance Computing (HPC) implementation of fire models, and artificial intelligence tools need to be integrated to build up a modern fire emergency response system. We propose a system architecture that provides the framework for integration of the various technologies. We describe the components of the generic FireGrid system architecture in detail. Finally we present a small-scale demonstration experiment which has been completed to highlight the concept and application of the FireGrid system to an actual fire. Although our proposed system architecture provides a versatile framework for integration, a number of new and interesting research problems need to be solved before actual deployment of the system. We outline some of the challenges involved which require significant interdisciplinary collaborations. JF - 9th Symposium of the International Association for Fire Safety Science (IAFSS) PB - IAFSS CY - Karlsruhe, GERMANY ER - TY - CONF T1 - OGSA-DAI: Middleware for Data Integration: Selected Applications T2 - ESCIENCE '08: Proceedings of the 2008 Fourth IEEE International Conference on eScience Y1 - 2008 A1 - Grant, Alistair A1 - Antonioletti, Mario A1 - Hume, Alastair C. A1 - Krause, Amy A1 - Dobrzelecki, Bartosz A1 - Jackson, Michael J. A1 - Parsons, Mark A1 - Atkinson, Malcolm P. A1 - Theocharopoulos, Elias JF - ESCIENCE '08: Proceedings of the 2008 Fourth IEEE International Conference on eScience PB - IEEE Computer Society CY - Washington, DC, USA SN - 978-0-7695-3535-7 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 - 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 - 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 - FireGrid: Integrated emergency response and fire safety engineering for the future built environment T2 - All Hands Meeting 2005 Y1 - 2006 A1 - D. Berry A1 - Usmani, A. A1 - Torero, J. A1 - Tate, A. A1 - McLaughlin, S. A1 - Potter, S. A1 - Trew, A. A1 - Baxter, R. A1 - Bull, M. A1 - Atkinson, M. AB - Analyses of disasters such as the Piper Alpha explosion (Sylvester-Evans and Drysdale, 1998), the World Trade Centre collapse (Torero et al, 2002, Usmani et al, 2003) and the fires at Kings Cross (Drysdale et al, 1992) and the Mont Blanc tunnel (Rapport Commun, 1999) have revealed many mistaken decisions, such as that which sent 300 fire-fighters to their deaths in the World Trade Centre. Many of these mistakes have been attributed to a lack of information about the conditions within the fire and the imminent consequences of the event. E-Science offers an opportunity to significantly improve the intervention in fire emergencies. The FireGrid Consortium is working on a mixture of research projects to make this vision a reality. This paper describes the research challenges and our plans for solving them. JF - All Hands Meeting 2005 CY - Nottingham, UK 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 - 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 - 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 - 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 - Heuristic Colour Assignment Strategies for Merge Models in Graph Colouring T2 - Springer Lecture Notes on Computer Science Y1 - 2005 A1 - Juhos, I. A1 - Tóth, A. A1 - van Hemert, J. I. ED - G. Raidl ED - J. Gottlieb KW - constraint satisfaction KW - graph colouring AB - In this paper, we combine a powerful representation for graph colouring problems with different heuristic strategies for colour assignment. Our novel strategies employ heuristics that exploit information about the partial colouring in an aim to improve performance. An evolutionary algorithm is used to drive the search. We compare the different strategies to each other on several very hard benchmarks and on generated problem instances, and show where the novel strategies improve the efficiency. JF - Springer Lecture Notes on Computer Science PB - Springer-Verlag, Berlin 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 - JOUR T1 - Web Service Grids: an evolutionary approach JF - Concurrency - Practice and Experience Y1 - 2005 A1 - Atkinson, Malcolm P. A1 - Roure, David De A1 - Dunlop, Alistair N. A1 - Fox, Geoffrey A1 - Henderson, Peter A1 - Hey, Anthony J. G. A1 - Paton, Norman W. A1 - Newhouse, Steven A1 - Parastatidis, Savas A1 - Trefethen, Anne E. A1 - Watson, Paul A1 - Webber, Jim VL - 17 ER - TY - CONF T1 - Binary Merge Model Representation of the Graph Colouring Problem T2 - Springer Lecture Notes on Computer Science Y1 - 2004 A1 - Juhos, I. A1 - Tóth, A. A1 - van Hemert, J. I. ED - J. Gottlieb ED - G. Raidl KW - constraint satisfaction KW - graph colouring AB - This paper describes a novel representation and ordering model that aided by an evolutionary algorithm, is used in solving the graph \emph{k}-colouring problem. Its strength lies in reducing the search space by breaking symmetry. An empirical comparison is made with two other algorithms on a standard suit of problem instances and on a suit of instances in the phase transition where it shows promising results. JF - Springer Lecture Notes on Computer Science PB - Springer-Verlag, Berlin SN - 3-540-21367-8 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 - RPRT T1 - Web Service Grids: An Evolutionary Approach Y1 - 2004 A1 - Malcolm Atkinson A1 - Roure, David De A1 - Alistair Dunlop A1 - Fox, Geoffrey A1 - Henderson, Peter A1 - Tony Hey A1 - Norman Paton A1 - Newhouse, Steven A1 - Parastatidis, Savas A1 - Anne Trefethen A1 - Watson, Paul A1 - Webber, Jim AB - The UK e-Science Programme is a £250M, 5 year initiative which has funded over 100 projects. These application-led projects are under-pinned by an emerging set of core middleware services that allow the coordinated, collaborative use of distributed resources. This set of middleware services runs on top of the research network and beneath the applications we call the ‘Grid’. Grid middleware is currently in transition from pre-Web Service versions to a new version based on Web Services. Unfortunately, only a very basic set of Web Services embodied in the Web Services Interoperability proposal, WS-I, are agreed by most IT companies. IBM and others have submitted proposals for Web Services for Grids - the Web Services ResourceFramework and Web Services Notification specifications - to the OASIS organisation for standardisation. This process could take up to 12 months from March 2004 and the specifications are subject to debate and potentially significant changes. Since several significant UK e-Science projects come to an end before the end of this process, the UK therefore needs to develop a strategy that will protect the UK’s investment in Grid middleware by informing the Open Middleware Infrastructure Institute’s (OMII) roadmap and UK middleware repository in Southampton. This paper sets out an evolutionary roadmap that will allow us to capture generic middleware components from projects in a form that will facilitate migration or interoperability with the emerging Grid Web Services standards and with on-going OGSA developments. In this paper we therefore define a set of Web Services specifications - that we call ‘WS-I+’ to reflect the fact that this is a larger set than currently accepted by WS-I – that we believe will enable us to achieve the twin goals of capturing these components and facilitating migration to future standards. We believe that the extra Web Services specifications we have included in WS-I+ are both helpful in building e-Science Grids and likely to be widely accepted. JF - UK e-Science Technical Report Series 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 - A new permutation model for solving the graph k-coloring problem T2 - Kalmàr Workshop on Logic and Computer Science Y1 - 2003 A1 - Juhos, I. A1 - Tóth, A. A1 - Tezuka, M. A1 - Tann, P. A1 - van Hemert, J. I. KW - constraint satisfaction KW - graph colouring AB - This paper describes a novel representation and ordering model, that is aided by an evolutionary algorithm, is used in solving the graph k-coloring. A comparison is made between the new representation and an improved version of the traditional graph coloring technique DSATUR on an extensive list of graph k-coloring problem instances with different properties. The results show that our model outperforms the improved DSATUR on most of the problem instances. JF - Kalmàr Workshop on Logic and Computer Science 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 - Adaptive Genetic Programming Applied to New and Existing Simple Regression Problems T2 - Springer Lecture Notes on Computer Science Y1 - 2001 A1 - Eggermont, J. A1 - van Hemert, J. I. ED - J. Miller ED - Tomassini, M. ED - P. L. Lanzi ED - C. Ryan ED - A. G. B. Tettamanzi ED - W. B. Langdon KW - data mining AB - In this paper we continue our study on adaptive genetic pro-gramming. We use Stepwise Adaptation of Weights to boost performance of a genetic programming algorithm on simple symbolic regression problems. We measure the performance of a standard GP and two variants of SAW extensions on two different symbolic regression prob-lems from literature. Also, we propose a model for randomly generating polynomials which we then use to further test all three GP variants. JF - Springer Lecture Notes on Computer Science PB - Springer-Verlag, Berlin SN - 9-783540-418993 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 -