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 - Lesion Area Detection Using Source Image Correlation Coefficient for CT Perfusion Imaging JF - IEEE Journal of Biomedical and Health Informatics Y1 - 2013 A1 - Fan Zhu A1 - Rodríguez, David A1 - Carpenter, Trevor K. A1 - Atkinson, Malcolm P. A1 - Wardlaw, Joanna M. KW - CT , Pattern Recognition , Perfusion Source Images , Segmentation AB - Computer tomography (CT) perfusion imaging is widely used to calculate brain hemodynamic quantities such as Cerebral Blood Flow (CBF), Cerebral Blood Volume (CBV) and Mean Transit Time (MTT) that aid the diagnosis of acute stroke. Since perfusion source images contain more information than hemodynamic maps, good utilisation of the source images can lead to better understanding than the hemodynamic maps alone. Correlation-coefficient tests are used in our approach to measure the similarity between healthy tissue time-concentration curves and unknown curves. This information is then used to differentiate penumbra and dead tissues from healthy tissues. The goal of the segmentation is to fully utilize information in the perfusion source images. Our method directly identifies suspected abnormal areas from perfusion source images and then delivers a suggested segmentation of healthy, penumbra and dead tissue. This approach is designed to handle CT perfusion images, but it can also be used to detect lesion areas in MR perfusion images. VL - 17 IS - 5 ER - TY - 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 - Computed Tomography Perfusion Imaging Denoising Using Gaussian Process Regression JF - Physics in Medicine and Biology Y1 - 2012 A1 - Fan Zhu A1 - Carpenter, Trevor A1 - Rodríguez, David A1 - Malcolm Atkinson A1 - Wardlaw, Joanna AB - Objective: Brain perfusion weighted images acquired using dynamic contrast studies have an important clinical role in acute stroke diagnosis and treatment decisions. However, Computed Tomography (CT) images suffer from low contrast-to-noise ratios (CNR) as a consequence of the limitation of the exposure to radiation of the patient. As a consequence, the developments of methods for improving the CNR are valuable. Methods: The majority of existing approaches for denoising CT images are optimized for 3D (spatial) information, including spatial decimation (spatially weighted mean filters) and techniques based on wavelet and curvelet transforms. However, perfusion imaging data is 4D as it also contains temporal information. Our approach using Gaussian process regression (GPR), which takes advantage of the temporal information, to reduce the noise level. Results: Over the entire image, GPR gains a 99% CNR improvement over the raw images and also improves the quality of haemodynamic maps allowing a better identification of edges and detailed information. At the level of individual voxel, GPR provides a stable baseline, helps us to identify key parameters from tissue time- concentration curves and reduces the oscillations in the curve. Conclusion: GPR is superior to the comparable techniques used in this study. ER - TY - 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 - Parallel perfusion imaging processing using GPGPU JF - Computer Methods and Programs in Biomedicine Y1 - 2012 A1 - Fan Zhu A1 - Rodríguez, David A1 - Carpenter, Trevor A1 - Malcolm Atkinson A1 - Wardlaw, Joanna KW - Deconvolution KW - GPGPU KW - Local AIF KW - Parallelization KW - Perfusion Imaging AB - Background and purpose The objective of brain perfusion quantification is to generate parametric maps of relevant hemodynamic quantities such as cerebral blood flow (CBF), cerebral blood volume (CBV) and mean transit time (MTT) that can be used in diagnosis of acute stroke. These calculations involve deconvolution operations that can be very computationally expensive when using local Arterial Input Functions (AIF). As time is vitally important in the case of acute stroke, reducing the analysis time will reduce the number of brain cells damaged and increase the potential for recovery. Methods GPUs originated as graphics generation dedicated co-processors, but modern GPUs have evolved to become a more general processor capable of executing scientific computations. It provides a highly parallel computing environment due to its large number of computing cores and constitutes an affordable high performance computing method. In this paper, we will present the implementation of a deconvolution algorithm for brain perfusion quantification on GPGPU (General Purpose Graphics Processor Units) using the CUDA programming model. We present the serial and parallel implementations of such algorithms and the evaluation of the performance gains using GPUs. Results Our method has gained a 5.56 and 3.75 speedup for CT and MR images respectively. Conclusions It seems that using GPGPU is a desirable approach in perfusion imaging analysis, which does not harm the quality of cerebral hemodynamic maps but delivers results faster than the traditional computation. UR - http://www.sciencedirect.com/science/article/pii/S0169260712001587 ER - TY - Generic T1 - A Review of Attacks and Security Approaches in Open Multi-agent Systems Y1 - 2012 A1 - Shahriar Bijani A1 - David Robertson AB - Open multi-agent systems (MASs) have growing popularity in the Multi-agent Systems community and are predicted to have many applications in future, as large scale distributed systems become more widespread. A major practical limitation to open MASs is security because the openness of such systems negates many traditional security solutions. In this paper we introduce and classify main attacks on open MASs. We then survey and analyse various security techniques in the literature and categorise them under prevention and detection approaches. Finally, we suggest which security technique is an appropriate countermeasure for which classes of attack. ER - TY - CONF T1 - The Use of Reputation as Noise-resistant Selection Bias in a Co-evolutionary Multi-agent System T2 - Genetic and Evolutionary Computation Conference Y1 - 2012 A1 - Nikolaos Chatzinikolaou A1 - Dave Robertson JF - Genetic and Evolutionary Computation Conference CY - Philadelphia ER - TY - Generic T1 - Intrusion Detection in Open Peer-to-Peer Multi-agent Systems T2 - 5th International Conference on Autonomous Infrastructure, Management and Security (AIMS 2011) Y1 - 2011 A1 - Shahriar Bijani A1 - David Robertson AB - One way to build large-scale autonomous systems is to develop open peer-to-peer architectures in which peers are not pre-engineered to work together and in which peers themselves determine the social norms that govern collective behaviour. A major practical limitation to such systems is security because the very openness of such systems negates most traditional security solutions. We propose a programme of research that addresses this problem by devising ways of attack detection and damage limitation that take advantage of social norms described by electronic institutions. We have analysed security issues of open peer-to-peer multi-agent systems and focused on probing attacks against confidentiality. We have proposed a framework and adapted an inference system, which shows the possibility of private information disclosure by an adversary. We shall suggest effective countermeasures in such systems and propose attack response techniques to limit possible damages. JF - 5th International Conference on Autonomous Infrastructure, Management and Security (AIMS 2011) T3 - Managing the dynamics of networks and services PB - Springer-Verlag Berlin SN - 978-3-642-21483-7 ER - TY - CONF T1 - A Parallel Deconvolution Algorithm in Perfusion Imaging T2 - Healthcare Informatics, Imaging, and Systems Biology (HISB) Y1 - 2011 A1 - Zhu, Fan. A1 - Rodríguez, David A1 - Carpenter, Trevor A1 - Malcolm Atkinson A1 - Wardlaw, Joanna KW - Deconvolution KW - GPGPU KW - Parallelization KW - Perfusion Imaging AB - In this paper, we will present the implementation of a deconvolution algorithm for brain perfusion quantification on GPGPU (General Purpose Graphics Processor Units) using the CUDA programming model. GPUs originated as graphics generation dedicated co-processors, but the modern GPUs have evolved to become a more general processor capable of executing scientific computations. It provides a highly parallel computing environment due to its huge number of computing cores and constitutes an affordable high performance computing method. The objective of brain perfusion quantification is to generate parametric maps of relevant haemodynamic quantities such as Cerebral Blood Flow (CBF), Cerebral Blood Volume (CBV) and Mean Transit Time (MTT) that can be used in diagnosis of conditions such as stroke or brain tumors. These calculations involve deconvolution operations that in the case of using local Arterial Input Functions (AIF) can be very expensive computationally. We present the serial and parallel implementations of such algorithm and the evaluation of the performance gains using GPUs. JF - Healthcare Informatics, Imaging, and Systems Biology (HISB) CY - San Jose, California SN - 978-1-4577-0325-6 UR - http://ieeexplore.ieee.org/xpls/abs_all.jsp?arnumber=6061411&tag=1 ER - TY - Generic T1 - Probing Attacks on Multi-agent Systems using Electronic Institutions T2 - Declarative Agent Languages and Technologies Workshop (DALT), AAMAS 2011 Y1 - 2011 A1 - Shahriar Bijani A1 - David Robertson A1 - David Aspinall JF - Declarative Agent Languages and Technologies Workshop (DALT), AAMAS 2011 ER - TY - CONF T1 - RapidBrain: Developing a Portal for Brain Research Imaging T2 - All Hands Meeting 2011, York Y1 - 2011 A1 - Kenton D'Mellow A1 - Rodríguez, David A1 - Carpenter, Trevor A1 - Jos Koetsier A1 - Dominic Job A1 - van Hemert, Jano A1 - Wardlaw, Joanna A1 - Fan Zhu AB - Brain imaging researchers execute complex multistep workflows in their computational analysis. Those workflows often include applications that have very different user interfaces and sometimes use different data formats. A good example is the brain perfusion quantification workflow used at the BRIC (Brain Research Imaging Centre) in Edinburgh. Rapid provides an easy method for creating portlets for computational jobs, and at the same it is extensible. We have exploited this extensibility with additions that stretch the functionality beyond the original limits. These changes can be used by other projects to create their own portals, but it should be noted that the development of such portals involve a greater effort than the required in the regular use of Rapid for creating portlets. In our case it has been used to provide a user-friendly interface for perfusion analysis that covers from volume JF - All Hands Meeting 2011, York CY - York ER - TY - JOUR T1 - A user-friendly web portal for T-Coffee on supercomputers JF - BMC Bioinformatics Y1 - 2011 A1 - J. Rius A1 - F. Cores A1 - F. Solsona A1 - van Hemert, J. I. A1 - Koetsier, J. A1 - C. Notredame KW - e-Science KW - portal KW - rapid AB - Background Parallel T-Coffee (PTC) was the first parallel implementation of the T-Coffee multiple sequence alignment tool. It is based on MPI and RMA mechanisms. Its purpose is to reduce the execution time of the large-scale sequence alignments. It can be run on distributed memory clusters allowing users to align data sets consisting of hundreds of proteins within a reasonable time. However, most of the potential users of this tool are not familiar with the use of grids or supercomputers. Results In this paper we show how PTC can be easily deployed and controlled on a super computer architecture using a web portal developed using Rapid. Rapid is a tool for efficiently generating standardized portlets for a wide range of applications and the approach described here is generic enough to be applied to other applications, or to deploy PTC on different HPC environments. Conclusions The PTC portal allows users to upload a large number of sequences to be aligned by the parallel version of TC that cannot be aligned by a single machine due to memory and execution time constraints. The web portal provides a user-friendly solution. VL - 12 UR - http://www.biomedcentral.com/1471-2105/12/150 ER - TY - JOUR T1 - 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 - RPRT T1 - Data-Intensive Research Workshop (15-19 March 2010) Report Y1 - 2010 A1 - Malcolm Atkinson A1 - Roure, David De A1 - van Hemert, Jano A1 - Shantenu Jha A1 - Ruth McNally A1 - Robert Mann A1 - Stratis Viglas A1 - Chris Williams KW - Data-intensive Computing KW - Data-Intensive Machines KW - Machine Learning KW - Scientific Databases AB - We met at the National e-Science Institute in Edinburgh on 15-19 March 2010 to develop our understanding of DIR. Approximately 100 participants (see Appendix A) worked together to develop their own understanding, and we are offering this report as the first step in communicating that to a wider community. We present this in turns of our developing/emerging understanding of "What is DIR?" and "Why it is important?'". We then review the status of the field, report what the workshop achieved and what remains as open questions. JF - National e-Science Centre PB - Data-Intensive Research Group, School of Informatics, University of Edinburgh CY - Edinburgh 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 - An open source toolkit for medical imaging de-identification JF - European Radiology Y1 - 2010 A1 - Rodríguez, David A1 - Carpenter, Trevor K. A1 - van Hemert, Jano I. A1 - Wardlaw, Joanna M. KW - Anonymisation KW - Data Protection Act (DPA) KW - De-identification KW - Digital Imaging and Communications in Medicine (DICOM) KW - Privacy policies KW - Pseudonymisation KW - Toolkit AB - Objective Medical imaging acquired for clinical purposes can have several legitimate secondary uses in research projects and teaching libraries. No commonly accepted solution for anonymising these images exists because the amount of personal data that should be preserved varies case by case. Our objective is to provide a flexible mechanism for anonymising Digital Imaging and Communications in Medicine (DICOM) data that meets the requirements for deployment in multicentre trials. Methods We reviewed our current de-identification practices and defined the relevant use cases to extract the requirements for the de-identification process. We then used these requirements in the design and implementation of the toolkit. Finally, we tested the toolkit taking as a reference those requirements, including a multicentre deployment. Results The toolkit successfully anonymised DICOM data from various sources. Furthermore, it was shown that it could forward anonymous data to remote destinations, remove burned-in annotations, and add tracking information to the header. The toolkit also implements the DICOM standard confidentiality mechanism. Conclusion A DICOM de-identification toolkit that facilitates the enforcement of privacy policies was developed. It is highly extensible, provides the necessary flexibility to account for different de-identification requirements and has a low adoption barrier for new users. VL - 20 UR - http://www.springerlink.com/content/j20844338623m167/ IS - 8 ER - TY - 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 - 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 - JOUR T1 - A Strategy for Research and Innovation in the Century of Information JF - Prometheus Y1 - 2009 A1 - e-Science Directors’ Forum Strategy Working Group A1 - Atkinson, M. A1 - Britton, D. A1 - Coveney, P. A1 - De Roure, D A1 - Garnett, N. A1 - Geddes, N. A1 - Gurney, R. A1 - Haines, K. A1 - Hughes, L. A1 - Ingram, D. A1 - Jeffreys, P. A1 - Lyon, L. A1 - Osborne, I. A1 - Perrott, P. A1 - Procter. R. A1 - Rusbridge, C. AB - More data will be produced in the next five years than in the entire history of human kind, a digital deluge that marks the beginning of the Century of Information. Through a year‐long consultation with UK researchers, a coherent strategy has been developed, which will nurture Century‐of‐Information Research (CIR); it crystallises the ideas developed by the e‐Science Directors’ Forum Strategy Working Group. This paper is an abridged version of their latest report which can be found at: http://wikis.nesc.ac.uk/escienvoy/Century_of_Information_Research_Strategy which also records the consultation process and the affiliations of the authors. This document is derived from a paper presented at the Oxford e‐Research Conference 2008 and takes into account suggestions made in the ensuing panel discussion. The goals of the CIR Strategy are to facilitate the growth of UK research and innovation that is data and computationally intensive and to develop a new culture of ‘digital‐systems judgement’ that will equip research communities, businesses, government and society as a whole, with the skills essential to compete and prosper in the Century of Information. The CIR Strategy identifies a national requirement for a balanced programme of coordination, research, infrastructure, translational investment and education to empower UK researchers, industry, government and society. The Strategy is designed to deliver an environment which meets the needs of UK researchers so that they can respond agilely to challenges, can create knowledge and skills, and can lead new kinds of research. It is a call to action for those engaged in research, those providing data and computational facilities, those governing research and those shaping education policies. The ultimate aim is to help researchers strengthen the international competitiveness of the UK research base and increase its contribution to the economy. The objectives of the Strategy are to better enable UK researchers across all disciplines to contribute world‐leading fundamental research; to accelerate the translation of research into practice; and to develop improved capabilities, facilities and context for research and innovation. It envisages a culture that is better able to grasp the opportunities provided by the growing wealth of digital information. Computing has, of course, already become a fundamental tool in all research disciplines. The UK e‐Science programme (2001–06)—since emulated internationally—pioneered the invention and use of new research methods, and a new wave of innovations in digital‐information technologies which have enabled them. The Strategy argues that the UK must now harness and leverage its own, plus the now global, investment in digital‐information technology in order to spread the benefits as widely as possible in research, education, industry and government. Implementing the Strategy would deliver the computational infrastructure and its benefits as envisaged in the Science & Innovation Investment Framework 2004–2014 (July 2004), and in the reports developing those proposals. To achieve this, the Strategy proposes the following actions: 1. support the continuous innovation of digital‐information research methods; 2. provide easily used, pervasive and sustained e‐Infrastructure for all research; 3. enlarge the productive research community which exploits the new methods efficiently; 4. generate capacity, propagate knowledge and develop skills via new curricula; and 5. develop coordination mechanisms to improve the opportunities for interdisciplinary research and to make digital‐infrastructure provision more cost effective. To gain the best value for money strategic coordination is required across a broad spectrum of stakeholders. A coherent strategy is essential in order to establish and sustain the UK as an international leader of well‐curated national data assets and computational infrastructure, which is expertly used to shape policy, support decisions, empower researchers and to roll out the results to the wider benefit of society. The value of data as a foundation for wellbeing and a sustainable society must be appreciated; national resources must be more wisely directed to the collection, curation, discovery, widening access, analysis and exploitation of these data. Every researcher must be able to draw on skills, tools and computational resources to develop insights, test hypotheses and translate inventions into productive use, or to extract knowledge in support of governmental decision making. This foundation plus the skills developed will launch significant advances in research, in business, in professional practice and in government with many consequent benefits for UK citizens. The Strategy presented here addresses these complex and interlocking requirements. VL - 27 ER - TY - JOUR T1 - Distributed Computing Education, Part 1: A Special Case? JF - IEEE Distributed Systems Online Y1 - 2008 A1 - Fergusson, D. A1 - Hopkins, R. A1 - Romano, D. A1 - Vander Meer, E. A1 - Atkinson, M. VL - 9 UR - http://dsonline.computer.org/portal/site/dsonline/menuitem.9ed3d9924aeb0dcd82ccc6716bbe36ec/index.jsp?&pName=dso_level1&path=dsonline/2008/06&file=o6002edu.xml&xsl=article.xsl&;jsessionid=LZ5zjySvc2xPnVv4qTYJXhlvwSnRGGj7S7WvPtrPyv23rJGQdjJr!982319602 IS - 6 ER - TY - JOUR T1 - Distributed Computing Education, Part 2: International Summer Schools JF - IEEE Distributed Systems Online Y1 - 2008 A1 - Fergusson, D. A1 - Hopkins, R. A1 - Romano, D. A1 - Vander Meer, E. A1 - Atkinson, M. VL - 9 UR - http://dsonline.computer.org/portal/site/dsonline/menuitem.9ed3d9924aeb0dcd82ccc6716bbe36ec/index.jsp?&pName=dso_level1&path=dsonline/2008/07&file=o7002edu.xml&xsl=article.xsl& IS - 7 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 - Fostering e-Infrastructures: from user-designer relations to community engagement T2 - Symposium on Project Management in e-Science Y1 - 2008 A1 - Voss, A. A1 - Asgari-Targhi, M. A1 - Halfpenny, P. A1 - Procter, R. A1 - Anderson, S. A1 - Dunn, S. A1 - Fragkouli, E. A1 - Hughes, L. A1 - Atkinson, M. A1 - Fergusson, D. A1 - Mineter, M. A1 - Rodden, T. AB - In this paper we discuss how e-Science can draw on the findings, approaches and methods developed in other disciplines to foster e-Infrastructures for research. We also discuss the issue of making user involvement in IT development scale across an open ommunity of researchers and from single systems to distributed e-Infrastructures supporting collaborative research. JF - Symposium on Project Management in e-Science CY - Oxford 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 - Interaction as a Grounding for Peer to Peer Knowledge Sharing T2 - Advances in Web Semantics Y1 - 2007 A1 - Robertson, D. A1 - Walton, C. A1 - Barker, A. A1 - Besana, P. A1 - Chen-Burger, Y. A1 - Hassan, F. A1 - Lambert, D. A1 - Li, G. A1 - McGinnis, J A1 - Osman, N. A1 - Bundy, A. A1 - McNeill, F. A1 - van Harmelen, F. A1 - Sierra, C. A1 - Giunchiglia, F. JF - Advances in Web Semantics PB - LNCS-IFIP VL - 1 ER - TY - CONF T1 - 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 - Improving Graph Colouring Algorithms and Heuristics Using a Novel Representation T2 - Springer Lecture Notes on Computer Science Y1 - 2006 A1 - Juhos, I. A1 - van Hemert, J. I. ED - J. Gottlieb ED - G. Raidl KW - constraint satisfaction KW - graph colouring AB - We introduce a novel representation for the graph colouring problem, called the Integer Merge Model, which aims to reduce the time complexity of an algorithm. Moreover, our model provides useful information for guiding heuristics as well as a compact description for algorithms. To verify the potential of the model, we use it in dsatur, in an evolutionary algorithm, and in the same evolutionary algorithm extended with heuristics. An empiricial investigation is performed to show an increase in efficiency on two problem suites , a set of practical problem instances and a set of hard problem instances from the phase transition. JF - Springer Lecture Notes on Computer Science PB - Springer-Verlag ER - TY - CONF T1 - Neighborhood Searches for the Bounded Diameter Minimum Spanning Tree Problem Embedded in a VNS, EA, and ACO T2 - Proceedings of the Genetic and Evolutionary Computation Conference (GECCO 2006) Y1 - 2006 A1 - Gruber, M. A1 - van Hemert, J. I. A1 - Raidl, G. R. ED - Maarten Keijzer ED - et al KW - constraint satisfaction KW - evolutionary computation KW - variable neighbourhood search AB - We consider the Bounded Diameter Minimum Spanning Tree problem and describe four neighbourhood searches for it. They are used as local improvement strategies within a variable neighbourhood search (VNS), an evolutionary algorithm (EA) utilising a new encoding of solutions, and an ant colony optimisation (ACO).We compare the performance in terms of effectiveness between these three hybrid methods on a suite f popular benchmark instances, which contains instances too large to solve by current exact methods. Our results show that the EA and the ACO outperform the VNS on almost all used benchmark instances. Furthermore, the ACO yields most of the time better solutions than the EA in long-term runs, whereas the EA dominates when the computation time is strongly restricted. JF - Proceedings of the Genetic and Evolutionary Computation Conference (GECCO 2006) PB - ACM CY - Seattle, USA VL - 2 ER - TY - CONF T1 - The Digital Curation Centre: a vision for digital curation T2 - 2005 IEEE International Symposium on Mass Storage Systems and Technology Y1 - 2005 A1 - Rusbridge, C. A1 - P. Burnhill A1 - S. Ross A1 - P. Buneman A1 - D. Giaretta A1 - Lyon, L. A1 - Atkinson, M. AB - We describe the aims and aspirations for the Digital Curation Centre (DCC), the UK response to the realisation that digital information is both essential and fragile. We recognise the equivalence of preservation as "interoperability with the future", asserting that digital curation is concerned with "communication across time". We see the DCC as having relevance for present day data curation and for continuing data access for generations to come. We describe the structure and plans of the DCC, designed to support these aspirations and based on a view of world class research being developed into curation services, all of which are underpinned by outreach to the broadest community. JF - 2005 IEEE International Symposium on Mass Storage Systems and Technology PB - IEEE Computer Society CY - Sardinia, Italy SN - 0-7803-9228-0 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 - 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 - 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 - CONF T1 - Property analysis of symmetric travelling salesman problem instances acquired through evolution T2 - Springer Lecture Notes on Computer Science Y1 - 2005 A1 - van Hemert, J. I. ED - G. Raidl ED - J. Gottlieb KW - problem evolving KW - travelling salesman AB - We show how an evolutionary algorithm can successfully be used to evolve a set of difficult to solve symmetric travelling salesman problem instances for two variants of the Lin-Kernighan algorithm. Then we analyse the instances in those sets to guide us towards deferring general knowledge about the efficiency of the two variants in relation to structural properties of the symmetric travelling salesman problem. JF - Springer Lecture Notes on Computer Science PB - Springer-Verlag, Berlin 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 - 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 - 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 - 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 - 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 - CONF T1 - Comparing Classical Methods for Solving Binary Constraint Satisfaction Problems with State of the Art Evolutionary Computation T2 - Springer Lecture Notes on Computer Science Y1 - 2002 A1 - van Hemert, J. I. ED - S. Cagnoni ED - J. Gottlieb ED - E. Hart ED - M. Middendorf ED - G. Raidl KW - constraint satisfaction AB - Constraint Satisfaction Problems form a class of problems that are generally computationally difficult and have been addressed with many complete and heuristic algorithms. We present two complete algorithms, as well as two evolutionary algorithms, and compare them on randomly generated instances of binary constraint satisfaction prob-lems. We find that the evolutionary algorithms are less effective than the classical techniques. JF - Springer Lecture Notes on Computer Science PB - Springer-Verlag, Berlin ER - TY - 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 - CONF T1 - Evolutionary Computation in Constraint Satisfaction and Machine Learning --- An abstract of my PhD. T2 - Proceedings of the Brussels Evolutionary Algorithms Day (BEAD-2001) Y1 - 2001 A1 - van Hemert, J. I. ED - Anne Defaweux ED - Bernard Manderick ED - Tom Lenearts ED - Johan Parent ED - Piet van Remortel KW - constraint satisfaction KW - data mining JF - Proceedings of the Brussels Evolutionary Algorithms Day (BEAD-2001) PB - Vrije Universiteit Brussel (VUB) ER - TY - BOOK T1 - GRUMPS Summer Anthology, 2001 Y1 - 2001 A1 - Atkinson, M. A1 - Brown, M. A1 - Cargill, J. A1 - Crease, M. A1 - Draper, S. A1 - Evans, H. A1 - Gray, P. A1 - Mitchell, C. A1 - Ritchie, M. A1 - Thomas, R. AB - This is the first collection of papers from GRUMPS [http://grumps.dcs.gla.ac.uk]. The project only started up in February 2001, and this collection (frozen at 1 Sept 2001) shows that it got off to a productive start. Versions of some of these papers have been submitted to conferences and workshops: the website will have more information on publication status and history. GRUMPS decided to begin with a first study, partly to help the team coalesce. This involved installing two pieces of software in a first year computing science lab: one (the "UAR") to record a large volume of student actions at a low level with a view to mining them later, another (the "LSS") directly designed to assist tutor-student interaction. Some of the papers derive from that, although more are planned. Results from this first study can be found on the website. The project also has a link to UWA in Perth, Western Australia, where related software has already been developed and used as described in one of the papers. Another project strand concerns using handsets in lecture theatres to support interactivity there, as two other papers describe. As yet unrepresented in this collection, GRUMPS will also be entering the bioinformatics application area. The GRUMPS project operates on several levels. It is based in the field of Distributed Information Management (DIM), expecting to cover both mobile and static nodes, synchronous and detached clients, high and low volume data sources. The specific focus of the project (see the original proposal on the web site) is to address records of computational activity (where any such pre-existing usage might have extra record collection installed) and data experimentation, where the questions to be asked of the data emerge concurrently with data collection which will therefore be dynamically modifiable: a requirement that further pushes on the space of DIM. The level above concerns building and making usable tools for asking questions of the data, or rather of the activities that generate the data. Above that again is the application domain level: what the original computational activities serve, education and bioinformatics being two identified cases. The GRUMPS team is therefore multidisciplinary, from DIM architecture researchers to educational evaluators. The mix of papers reflects this. PB - Academic Press ER - TY - CHAP T1 - Persistence and Java — A Balancing Act T2 - Objects and Databases Y1 - 2001 A1 - Atkinson, M. ED - Klaus Dittrich ED - Giovanna Guerrini ED - Isabella Merlo ED - Marta Oliva ED - M. Elena Rodriguez AB - Large scale and long-lived application systems, enterprise applications, require persistence, that is provision of storage for many of their data structures. The JavaTM programming language is a typical example of a strongly-typed, object-oriented programming language that is becoming popular for building enterprise applications. It therefore needs persistence. The present options for obtaining this persistence are reviewed. We conclude that the Orthogonal Persistence Hypothesis, OPH, is still persuasive. It states that the universal and automated provision of longevity or brevity for all data will significantly enhance developer productivity and improve applications. This position paper reports on the PJama project with particular reference to its test of the OPH. We review why orthogonal persistence has not been taken up widely, and why the OPH is still incompletely tested. This leads to a more general challenge of how to conduct experiments which reveal large-scale and long-term effects and some thoughts on how that challenge might be addressed by the software research community. JF - Objects and Databases T3 - Lecture Notes in Computer Science PB - Springer VL - 1944 UR - http://www.springerlink.com/content/8t7x3m1ehtdqk4bm/?p=7ece1338fff3480b83520df395784cc6&pi=0 ER -