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 - 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 - EnzML: multi-label prediction of enzyme classes using InterPro signatures. JF - BMC Bioinformatics Y1 - 2012 A1 - De Ferrari, Luna A1 - Stuart Aitken A1 - van Hemert, Jano A1 - Goryanin, Igor AB - BACKGROUND: Manual annotation of enzymatic functions cannot keep up with automatic genome sequencing. In this work we explore the capacity of InterPro sequence signatures to automatically predict enzymatic function. RESULTS: We present EnzML, a multi-label classification method that can efficiently account also for proteins with multiple enzymatic functions: 50,000 in UniProt. EnzML was evaluated using a standard set of 300,747 proteins for which the manually curated Swiss-Prot and KEGG databases have agreeing Enzyme Commission (EC) annotations. EnzML achieved more than 98% subset accuracy (exact match of all correct Enzyme Commission classes of a protein) for the entire dataset and between 87 and 97% subset accuracy in reannotating eight entire proteomes: human, mouse, rat, mouse-ear cress, fruit fly, the S. pombe yeast, the E. coli bacterium and the M. jannaschii archaebacterium. To understand the role played by the dataset size, we compared the cross-evaluation results of smaller datasets, either constructed at random or from specific taxonomic domains such as archaea, bacteria, fungi, invertebrates, plants and vertebrates. The results were confirmed even when the redundancy in the dataset was reduced using UniRef100, UniRef90 or UniRef50 clusters. CONCLUSIONS: InterPro signatures are a compact and powerful attribute space for the prediction of enzymatic function. This representation makes multi-label machine learning feasible in reasonable time (30 minutes to train on 300,747 instances with 10,852 attributes and 2,201 class values) using the Mulan Binary Relevance Nearest Neighbours algorithm implementation (BR-kNN). VL - 13 ER - TY - JOUR T1 - Managing dynamic enterprise and urgent workloads on clouds using layered queuing and historical performance models JF - Simulation Modelling Practice and Theory Y1 - 2011 A1 - David A. Bacigalupo A1 - van Hemert, Jano I. A1 - Xiaoyu Chen A1 - Asif Usmani A1 - Adam P. Chester A1 - Ligang He A1 - Donna N. Dillenberger A1 - Gary B. Wills A1 - Lester Gilbert A1 - Stephen A. Jarvis KW - e-Science AB - The automatic allocation of enterprise workload to resources can be enhanced by being able to make what–if response time predictions whilst different allocations are being considered. We experimentally investigate an historical and a layered queuing performance model and show how they can provide a good level of support for a dynamic-urgent cloud environment. Using this we define, implement and experimentally investigate the effectiveness of a prediction-based cloud workload and resource management algorithm. Based on these experimental analyses we: (i) comparatively evaluate the layered queuing and historical techniques; (ii) evaluate the effectiveness of the management algorithm in different operating scenarios; and (iii) provide guidance on using prediction-based workload and resource management. VL - 19 ER - TY - CONF T1 - 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 - 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 - CONF T1 - Resource management of enterprise cloud systems using layered queuing and historical performance models T2 - IEEE International Symposium on Parallel Distributed Processing Y1 - 2010 A1 - Bacigalupo, D. A. A1 - van Hemert, J. A1 - Usmani, A. A1 - Dillenberger, D. N. A1 - Wills, G. B. A1 - Jarvis, S. A. KW - e-Science AB - The automatic allocation of enterprise workload to resources can be enhanced by being able to make `what-if' response time predictions, whilst different allocations are being considered. It is important to quantitatively compare the effectiveness of different prediction techniques for use in cloud infrastructures. To help make the comparison of relevance to a wide range of possible cloud environments it is useful to consider the following. 1.) urgent cloud customers such as the emergency services that can demand cloud resources at short notice (e.g. for our FireGrid emergency response software). 2.) dynamic enterprise systems, that must rapidly adapt to frequent changes in workload, system configuration and/or available cloud servers. 3.) The use of the predictions in a coordinated manner by both the cloud infrastructure and cloud customer management systems. 4.) A broad range of criteria for evaluating each technique. However, there have been no previous comparisons meeting these requirements. This paper, meeting the above requirements, quantitatively compares the layered queuing and (\^A¿HYDRA\^A¿) historical techniques - including our initial thoughts on how they could be combined. Supporting results and experiments include the following: i.) defining, investigating and hence providing guidelines on the use of a historical and layered queuing model; ii.) using these guidelines showing that both techniques can make low overhead and typically over 70% accurate predictions, for new server architectures for which only a small number of benchmarks have been run; and iii.) defining and investigating tuning a prediction-based cloud workload and resource management algorithm. JF - IEEE International Symposium on Parallel Distributed Processing ER - TY - CONF T1 - A model of social collaboration in Molecular Biology knowledge bases T2 - Proceedings of the 6th Conference of the European Social Simulation Association (ESSA'09) Y1 - 2009 A1 - De Ferrari, Luna A1 - Stuart Aitken A1 - van Hemert, Jano A1 - Goryanin, Igor AB - Manual annotation of biological data cannot keep up with data production. Open annotation models using wikis have been proposed to address this problem. In this empirical study we analyse 36 years of knowledge collection by 738 authors in two Molecular Biology wikis (EcoliWiki and WikiPathways) and two knowledge bases (OMIM and Reactome). We first investigate authorship metrics (authors per entry and edits per author) which are power-law distributed in Wikipedia and we find they are heavy-tailed in these four systems too. We also find surprising similarities between the open (editing open to everyone) and the closed systems (expert curators only). Secondly, to discriminate between driving forces in the measured distributions, we simulate the curation process and find that knowledge overlap among authors can drive the number of authors per entry, while the time the users spend on the knowledge base can drive the number of contributions per author. JF - Proceedings of the 6th Conference of the European Social Simulation Association (ESSA'09) PB - European Social Simulation Association 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 - Strategies and Policies to Support and Advance Education in e-Science JF - Computing Now Y1 - 2009 A1 - Malcolm Atkinson A1 - Elizabeth Vander Meer A1 - Fergusson, David A1 - Clive Davenhall A1 - Hamza Mehammed AB - In previous installments of this series, we’ve presented tools and resources that university undergraduate and graduate environments must provide to allow for the continued development and success of e-Science education. We’ve introduced related summer (http://doi.ieeecomputersociety.org/ 10.1109/MDSO.2008.20) and winter (http://doi.ieeecomputersociety.org/10.1109/MDSO.2008.26) schools and important issues such as t-Infrastructure provision (http://doi.ieeecomputersociety.org/ 10.1109/MDSO.2008.28), intellectual property rights in the context of digital repositories (http://doi.ieeecomputersociety.org/10.1109/MDSO.2008.34), and curriculum content (http://www2. computer.org/portal/web/computingnow/0309/education). We conclude now with an overview of areas in which we must focus effort and strategies and policies that could provide much-needed support in these areas. We direct these strategy and policy recommendations toward key stakeholders in e-Science education, such as ministries of education, councils in professional societies, and professional teachers and educational strategists. Ministries of education can influence funding councils, thus financially supporting our proposals. Professional societies can assist in curricula revision, and teachers and strategists shape curricula in institutions, which makes them valuable in improving and developing education in e-Science and (perhaps) e-Science in education. We envision incremental change in curricula, so our proposals aim to evolve existing courses, rather than suggesting drastic upheavals and isolated additions. The long-term goal is to ensure that every graduate obtains the appropriate level of e-Science competency for their field, but we don’t presume to define that level for any given discipline or institution. We set out issues and ideas but don’t offer rigid prescriptions, which would take control away from important stakeholders. UR - http://www.computer.org/portal/web/computingnow/education 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 - Generic T1 - European Graduate Student Workshop on Evolutionary Computation Y1 - 2008 A1 - Di Chio, Cecilia A1 - Giacobini, Mario A1 - van Hemert, Jano ED - Di Chio, Cecilia ED - Giacobini, Mario ED - van Hemert, Jano KW - evolutionary computation AB - Evolutionary computation involves the study of problem-solving and optimization techniques inspired by principles of evolution and genetics. As any other scientific field, its success relies on the continuity provided by new researchers joining the field to help it progress. One of the most important sources for new researchers is the next generation of PhD students that are actively studying a topic relevant to this field. It is from this main observation the idea arose of providing a platform exclusively for PhD students. 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 - 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 - Widening Uptake of e-Infrastructure Services T2 - 4th International Conference on e-Social Science Y1 - 2008 A1 - Voss, A. A1 - Asgari-Targhi, M. A1 - Procter, R. A1 - Halfpenny, P. A1 - Dunn, S. A1 - Fragkouli, E. A1 - Anderson, S. A1 - Hughes, L. A1 - Mineter, M. A1 - Fergusson, D. A1 - Atkinson, M. AB - This paper presents findings from the e-Uptake project which aims to widen the uptake of e-Infrastructure Services for research. We focus specifically on the identification of barriers and enablers of uptake and the taxonomy developed to structure our findings. Based on these findings, we describe the development of a number of interventions such as training and outreach events, workshops and the deployment of a UK 'one-stop-shop' for support and event information as well as training material. Finally, we will describe how the project relates to other ongoing community engagement efforts in the UK and worldwide. Introduction Existing investments in e-Science and Grid computing technologies have helped to develop the capacity to build e-Infrastructures for research: distributed, networked, interoperable computing and data resources that are available to underpin a wide range of research activities in all research disciplines. In the UK, the Research Councils and the JISC are funding programmes to support the development of essential components of such infrastructures such as National Grid Service (www.ngs.ac.uk) or the UK Access Management Federation (www.ukfederation.org.uk) as well as discipline-specific efforts to build consistent and accessible instantiations of e-Infrastructures, for example the e- Infrastructure for the Social Sciences (Daw et al. 2007). These investments are complemented by an active programme of community engagement (Voss et al. 2007). As part of the community engagement strand of its e-Infrastructure programme, JISC has funded the e-Uptake project, a collaboration between the ESRC National Centre for e-Social Science at the University of Manchester, the Arts & Humanities e-Science Support Centre at King's College London and the National e-Science Centre at the University of Edinburgh. In this paper we present the project's activities to date to widen the uptake of e-Infrastructure services by eliciting information about the barriers to and enablers of uptake, developing adequate interventions such as training and outreach events, running workshops and the deploying a UK 'one-stop-shop' for support and event information as well as training material. JF - 4th International Conference on e-Social Science CY - Manchester UR - http://www.ncess.ac.uk/events/conference/programme/workshop1/?ref=/programme/thurs/1aVoss.htm ER - TY - CONF T1 - WikiSim: simulating knowledge collection and curation in structured wikis. T2 - Proceedings of the 2008 International Symposium on Wikis in Porto, Portugal Y1 - 2008 A1 - De~Ferrari, Luna A1 - Stuart Aitken A1 - van Hemert, Jano A1 - Goryanin, Igor AB - The aim of this work is to model quantitatively one of the main properties of wikis: how high quality knowledge can emerge from the individual work of independent volunteers. The approach chosen is to simulate knowledge collection and curation in wikis. The basic model represents the wiki as a set of of true/false values, added and edited at each simulation round by software agents (users) following a fixed set of rules. The resulting WikiSim simulations already manage to reach distributions of edits and user contributions very close to those reported for Wikipedia. WikiSim can also span conditions not easily measurable in real-life wikis, such as the impact of various amounts of user mistakes. WikiSim could be extended to model wiki software features, such as discussion pages and watch lists, while monitoring the impact they have on user actions and consensus, and their effect on knowledge quality. The method could also be used to compare wikis with other curation scenarios based on centralised editing by experts. The future challenges for WikiSim will be to find appropriate ways to evaluate and validate the models and to keep them simple while still capturing relevant properties of wiki systems. JF - Proceedings of the 2008 International Symposium on Wikis in Porto, Portugal PB - ACM CY - New York, NY, USA ER - TY - CONF T1 - Accessing Data in Grids Using OGSA-DAI T2 - Knowledge and Data Management in Grids Y1 - 2007 A1 - Chue Hong, N. P. A1 - Antonioletti, M. A1 - Karasavvas, K. A. A1 - Atkinson, M. ED - Talia, D. ED - Bilas, A. ED - Dikaiakos, M. AB - The grid provides a vision in which resources, including storage and data, can be shared across organisational boundaries. The original emphasis of grid computing lay in the sharing of computational resources but technological and scientific advances have led to an ongoing data explosion in many fields. However, data is stored in many different storage systems and data formats, with different schema, access rights, metadata attributes, and ontologies all of which are obstacles to the access, integration and management of this information. In this chapter we examine some of the ways in which these differences can be addressed by grid technology to enable the meaningful sharing of data. In particular, we present an overview of the OGSA-DAI (Open Grid Service Architecture - Data Access and Integration) software, which provides a uniform, extensible framework for accessing structured and semi-structured data and provide some examples of its use in other projects. The open-source OGSA-DAI software is freely available from http://www.ogsadai.org.uk. JF - Knowledge and Data Management in Grids SN - 978-0-387-37830-5 UR - http://www.springer.com/computer/communication+networks/book/978-0-387-37830-5 ER - TY - CHAP T1 - COBrA and COBrA-CT: Ontology Engineering Tools T2 - Anatomy Ontologies for Bioinformatics: Principles and Practice Y1 - 2007 A1 - Stuart Aitken A1 - Yin Chen ED - Albert Burger ED - Duncan Davidson ED - Richard Baldock AB - COBrA is a Java-based ontology editor for bio-ontologies and anatomies that dif- fers from other editors by supporting the linking of concepts between two ontologies, and providing sophisticated analysis and verification functions. In addition to the Gene Ontology and Open Biology Ontologies formats, COBrA can import and export ontologies in the Se- mantic Web formats RDF, RDFS and OWL. COBrA is being re-engineered as a Prot ́eg ́e plug-in, and complemented by an ontology server and a tool for the management of ontology versions and collaborative ontology de- velopment. We describe both the original COBrA tool and the current developments in this chapter. JF - Anatomy Ontologies for Bioinformatics: Principles and Practice PB - Springer SN - ISBN-10:1846288843 UR - http://www.amazon.ca/Anatomy-Ontologies-Bioinformatics-Principles-Practice/dp/1846288843 ER - TY - CONF T1 - e-Research Infrastructure Development and Community Engagement T2 - All Hands Meeting 2007 Y1 - 2007 A1 - Voss, A. A1 - Mascord, M. A1 - Fraser, M. A1 - Jirotka, M. A1 - Procter, R. A1 - Halfpenny, P. A1 - Fergusson, D. A1 - Atkinson, M. A1 - Dunn, S. A1 - Blanke, T. A1 - Hughes, L. A1 - Anderson, S. AB - The UK and wider international e-Research initiatives are entering a critical phase in which they need to move from the development of the basic underlying technology, demonstrators, prototypes and early applications to wider adoption and the development of stable infrastructures. In this paper we will review existing work on studies of infrastructure and community development, requirements elicitation for existing services as well as work within the arts and humanities and the social sciences to establish e-Research in these communities. We then describe two projects recently funded by JISC to study barriers to adoption and responses to them as well as use cases and service usage models. JF - All Hands Meeting 2007 CY - Nottingham, UK 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 - Transaction-Based Grid Database Replication T2 - UK e-Science Al l Hands Meeting 2007 Y1 - 2007 A1 - Y. Chen A1 - D. Berry A1 - P. Dantressangle KW - Grid, Replication, Transaction-based, OGSA-DAI AB - We present a framework for grid database replication. Data replication is one of the most useful strategies to achieve high levels of availability and fault tolerance as well as minimal access time in grids. It is commonly demanded by many grid applications. However, most existing grid replication systems only deal with read-only files. By contrast, several relational database vendors provide tools that offer transaction-based replication, but the capabilities of these products are insufficient to address grid issues. They lack scalability and cannot cope with the heterogeneous nature of grid resources. Our approach uses existing grid mechanisms to provide a metadata registry and to make initial replicas of data resources. We then define high-level APIs for managing transaction-based replication. These APIs can be mapped to a variety of relational database replication mechanisms allowing us to use existing vendor-specific solutions. The next stage in the project will use OGSA- DAI to manage replication across multiple domains. In this way, our framework can support transaction-based database synchronisation that maintains consistency in a data-intensive, large- scale distributed, disparate networking environment. JF - UK e-Science Al l Hands Meeting 2007 CY - Nottingham, UK ER - TY - 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 - Complexity Transitions in Evolutionary Algorithms: Evaluating the impact of the initial population T2 - Proceedings of the Congress on Evolutionary Computation Y1 - 2005 A1 - Defaweux, A. A1 - Lenaerts, T. A1 - van Hemert, J. I. A1 - Parent, J. KW - constraint satisfaction KW - transition models AB - This paper proposes an evolutionary approach for the composition of solutions in an incremental way. The approach is based on the metaphor of transitions in complexity discussed in the context of evolutionary biology. Partially defined solutions interact and evolve into aggregations until a full solution for the problem at hand is found. The impact of the initial population on the outcome and the dynamics of the process is evaluated using the domain of binary constraint satisfaction problems. JF - Proceedings of the Congress on Evolutionary Computation PB - {IEEE} Press ER - TY - CONF T1 - Cross-Layer Peer-to-Peer Traffic Identification and Optimization Based on Active Networking T2 - 7th International Working Conference on Active and Programmable Networks Y1 - 2005 A1 - Dedinski, I. A1 - De Meer, H. A1 - Liangxiu Han A1 - Mathy, L. A1 - Pezaros, D. A1 - P. , Sventek, J. S. A1 - Xiaoying, Z. JF - 7th International Working Conference on Active and Programmable Networks CY - Sophia Antipolis, French Riviera, La Cote d'Azur, France, November 21-23, 2005. ER - TY - CONF T1 - Evolutionary Transitions as a Metaphor for Evolutionary Optimization T2 - LNAI 3630 Y1 - 2005 A1 - Defaweux, A. A1 - Lenaerts, T. A1 - van Hemert, J. I. ED - M. Capcarrere ED - A. A. Freitas ED - P. J. Bentley ED - C. G. Johnson ED - J. Timmis KW - constraint satisfaction KW - transition models AB - This paper proposes a computational model for solving optimisation problems that mimics the principle of evolutionary transitions in individual complexity. More specifically it incorporates mechanisms for the emergence of increasingly complex individuals from the interaction of more simple ones. The biological principles for transition are outlined and mapped onto an evolutionary computation context. The class of binary constraint satisfaction problems is used to illustrate the transition mechanism. JF - LNAI 3630 PB - Springer-Verlag SN - 3-540-28848-1 ER - TY - Generic T1 - Experience with the international testbed in the crossgrid project T2 - Advances in Grid Computing-EGC 2005 Y1 - 2005 A1 - Gomes, J. A1 - David, M. A1 - Martins, J. A1 - Bernardo, L. A1 - A García A1 - Hardt, M. A1 - Kornmayer, H. A1 - Marco, Jesus A1 - Marco, Rafael A1 - Rodríguez, David A1 - Diaz, Irma A1 - Cano, Daniel A1 - Salt, J. A1 - Gonzalez, S. A1 - J Sánchez A1 - Fassi, F. A1 - Lara, V. A1 - Nyczyk, P. A1 - Lason, P. A1 - Ozieblo, A. A1 - Wolniewicz, P. A1 - Bluj, M. A1 - K Nawrocki A1 - A Padee A1 - W Wislicki ED - Peter M. A. Sloot, Alfons G. Hoekstra, Thierry Priol, Alexander Reinefeld ED - Marian Bubak JF - Advances in Grid Computing-EGC 2005 T3 - LNCS PB - Springer Berlin/Heidelberg CY - Amsterdam VL - 3470 ER - TY - CONF T1 - OGSA-DAI Status and Benchmarks T2 - All Hands Meeting 2005 Y1 - 2005 A1 - Antonioletti, Mario A1 - Malcolm Atkinson A1 - Rob Baxter A1 - Andrew Borle A1 - Hong, Neil P. Chue A1 - Patrick Dantressangle A1 - Hume, Alastair C. A1 - Mike Jackson A1 - Krause, Amy A1 - Laws, Simon A1 - Parsons, Mark A1 - Paton, Norman W. A1 - Jennifer M. Schopf A1 - Tom Sugden A1 - Watson, Paul AB - This paper presents a status report on some of the highlights that have taken place within the OGSADAI project since the last AHM. A description of Release 6.0 functionality and details of the forthcoming release, due in September 2005, is given. Future directions for this project are discussed. This paper also describes initial results of work being done to systematically benchmark recent OGSADAI releases. The OGSA-DAI software distribution, and more information about the project, is available from the project website at www.ogsadai.org.uk. JF - All Hands Meeting 2005 CY - Nottingham, UK ER - TY - CONF T1 - Organization of the International Testbed of the CrossGrid Project T2 - Cracow Grid Workshop 2005 Y1 - 2005 A1 - Gomes, J. A1 - David, M. A1 - Martins, J. A1 - Bernardo, L. A1 - Garcia, A. A1 - Hardt, M. A1 - Kornmayer, H. A1 - Marco, Rafael A1 - Rodríguez, David A1 - Diaz, Irma A1 - Cano, Daniel A1 - Salt, J. A1 - Gonzalez, S. A1 - Sanchez, J. A1 - Fassi, F. A1 - Lara, V. A1 - Nyczyk, P. A1 - Lason, P. A1 - Ozieblo, A. A1 - Wolniewicz, P. A1 - Bluj, M. JF - Cracow Grid Workshop 2005 ER - TY - CONF T1 - Transition Models as an incremental approach for problem solving in Evolutionary Algorithms T2 - Proceedings of the Genetic and Evolutionary Computation Conference Y1 - 2005 A1 - Defaweux, A. A1 - Lenaerts, T. A1 - van Hemert, J. I. A1 - Parent, J. ED - H.-G. Beyer ED - et al KW - constraint satisfaction KW - transition models AB - This paper proposes an incremental approach for building solutions using evolutionary computation. It presents a simple evolutionary model called a Transition model. It lets building units of a solution interact and then uses an evolutionary process to merge these units toward a full solution for the problem at hand. The paper provides a preliminary study on the evolutionary dynamics of this model as well as an empirical comparison with other evolutionary techniques on binary constraint satisfaction. JF - Proceedings of the Genetic and Evolutionary Computation Conference PB - {ACM} Press 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 - Generic T1 - Grid Services Supporting the Usage of Secure Federated, Distributed Biomedical Data T2 - All Hands Meeting 2004 Y1 - 2004 A1 - Richard Sinnott A1 - Malcolm Atkinson A1 - Micha Bayer A1 - Dave Berry A1 - Anna Dominiczak A1 - Magnus Ferrier A1 - David Gilbert A1 - Neil Hanlon A1 - Derek Houghton A1 - Hunt, Ela A1 - David White AB - The BRIDGES project is a UK e-Science project that provides grid based support for biomedical research into the genetics of hypertension – the Cardiovascular Functional Genomics Project (CFG). Its main goal is to provide an effective environment for CFG, and biomedical research in general, including access to integrated data, analysis and visualization, with appropriate authorisation and privacy, as well as grid based computational tools and resources. It also aims to provide an improved understanding of the requirements of academic biomedical research virtual organizations and to evaluate the utility of existing data federation tools. JF - All Hands Meeting 2004 CY - Nottingham, UK UR - http://www.allhands.org.uk/2004/proceedings/papers/87.pdf ER - TY - CONF T1 - Grid-Based Metadata Services T2 - SSDBM Y1 - 2004 A1 - Deelman, Ewa A1 - Singh, Gurmeet Singh A1 - Atkinson, Malcolm P. A1 - Chervenak, Ann L. A1 - Hong, Neil P. Chue A1 - Kesselman, Carl A1 - Patil, Sonal A1 - Pearlman, Laura A1 - Su, Mei-Hui JF - SSDBM ER - TY - CONF T1 - OGSA-DAI Status Report and Future Directions T2 - All Hands Meeting 2004 Y1 - 2004 A1 - Antonioletti, Mario A1 - Malcolm Atkinson A1 - Rob Baxter A1 - Borley, Andrew A1 - Hong, Neil P. Chue A1 - Collins, Brian A1 - Jonathan Davies A1 - Desmond Fitzgerald A1 - Hardman, Neil A1 - Hume, Alastair C. A1 - Mike Jackson A1 - Krause, Amrey A1 - Laws, Simon A1 - Paton, Norman W. A1 - Tom Sugden A1 - Watson, Paul A1 - Mar AB - Data Access and Integration (DAI) of data resources, such as relational and XML databases, within a Grid context. Project members also participate in the development of DAI standards through the GGF DAIS WG. The standards that emerge through this effort will be adopted by OGSA-DAI once they have stabilised. The OGSA-DAI developers are also engaging with a growing user community to gather their data and functionality requirements. Several large projects are already using OGSA-DAI to provide their DAI capabilities. This paper presents a status report on OGSA-DAI activities since the last AHM and announces future directions. The OGSA-DAI software distribution and more information about the project is available from the project website at http://www.ogsadai.org.uk/. JF - All Hands Meeting 2004 CY - Nottingham, UK ER - TY - CONF T1 - 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 - RPRT T1 - Grid Database Access and Integration: Requirements and Functionalities Y1 - 2003 A1 - Atkinson, M. P. A1 - Dialani, V. A1 - Guy, L. A1 - Narang, I. A1 - Paton, N. W. A1 - Pearson, D. A1 - Storey, T. A1 - Watson, P. AB - This document is intended to provide the context for developing Grid data service standard recommendations within the Global Grid Forum. It defines the generic requirements for accessing and integrating persistent structured and semi-structured data. In addition, it defines the generic functionalities which a Grid data service needs to provide in supporting discovery of and controlled access to data, in performing data manipulation operations, and in virtualising data resources. The document also defines the scope of Grid data service standard recommendations which are presented in a separate document. JF - Global Grid Forum ER - TY - 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 - An Engineering Approach to Evolutionary Art T2 - Proceedings of the Genetic and Evolutionary Computation Conference (GECCO-2001) Y1 - 2001 A1 - van Hemert, J. I. A1 - Jansen, M. L. M. ED - Lee Spector ED - Erik D. Goodman ED - Annie Wu ED - W. B. Langdon ED - Hans-Michael Voigt ED - Mitsuo Gen ED - Sandip Sen ED - Marco Dorigo ED - Shahram Pezeshk ED - Max H. Garzon ED - Edmund Burke KW - evolutionary art AB - We present a general system that evolves art on the Internet. The system runs on a server which enables it to collect information about its usage world wide; its core uses operators and representations from genetic program-ming. We show two types of art that can be evolved using this general system. JF - Proceedings of the Genetic and Evolutionary Computation Conference (GECCO-2001) PB - Morgan Kaufmann Publishers, San Francisco ER - TY - 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 - CONF T1 - The GRUMPS Architecture: Run-time Evolution in a Large Scale Distributed System T2 - Proceedings of the Workshop on Engineering Complex Object-Oriented Solutions for Evolution (ECOOSE), held as part of OOPSLA 2001. Y1 - 2001 A1 - Evans, Huw A1 - Peter Dickman A1 - Malcolm Atkinson AB - This paper describes the first version of the distributed programming architecture for the Grumps1 project. The architecture consists of objects that communicate in terms of both asynchronous and synchronous events. A novel three-level extensible naming scheme is discussed that allows Grumps developers to deploy systems that can refer to entities not identified at the time when the Grumps system and application-level code were implemented. Examples detailing how the topology of a Grumps system may be changed at run-time and how new object implementations may be distributed during system execution are given. The separation of policy from mechanism is shown to be a major part of how system evolution is supported and this is made even more flexible when expressed through the use of Java interfaces for crucial core concepts. JF - Proceedings of the Workshop on Engineering Complex Object-Oriented Solutions for Evolution (ECOOSE), held as part of OOPSLA 2001. 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 - TY - CHAP T1 - Scalable and Recoverable Implementation of Object Evolution for the PJama1 Platform T2 - Persistent Object Systems: Design, Implementation, and Use 9th International Workshop, POS-9 Lillehammer, Norway, September 6–8, 2000 Revised Papers Y1 - 2001 A1 - Atkinson, M. P. A1 - Dmitriev, M. A. A1 - Hamilton, C. A1 - Printezis, T. ED - Graham N. C. ED - Kirby, Alan Dearle ED - Dag I. K. Sjøberg AB - PJama1 is the latest version of an orthogonally persistent platform for Java. It depends on a new persistent object store, Sphere, and provides facilities for class evolution. This evolution technology supports an arbitrary set of changes to the classes, which may have arbitrarily large populations of persistent objects. We verify that the changes are safe. When there are format changes, we also convert all of the instances, while leaving their identities unchanged. We aspire to both very large persistent object stores and freedom for developers to specify arbitrary conversion methods in Java to convey information from old to new formats. Evolution operations must be safe and the evolution cost should be approximately linear in the number of objects that must be reformatted. In order that these conversion methods can be written easily, we continue to present the pre-evolution state consistently to Java executions throughout an evolution. At the completion of applying all of these transformations, we must switch the store state to present only the post-evolution state, with object identity preserved. We present an algorithm that meets these requirements for eager, total conversion. This paper focuses on the mechanisms built into Sphere to support safe, atomic and scalable evolution. We report our experiences in using this technology and include a preliminary set of performance measurements. JF - Persistent Object Systems: Design, Implementation, and Use 9th International Workshop, POS-9 Lillehammer, Norway, September 6–8, 2000 Revised Papers T3 - Lecture Notes in Computer Science PB - Springer VL - 2135 UR - http://www.springerlink.com/content/09hx07h9lw0p1h82/?p=2bc20319905146bab8ba93b2fcc8cc01&pi=23 ER - TY - CONF T1 - Scalable and Recoverable Implementation of Object Evolution for the PJama1 Platform T2 - POS Y1 - 2000 A1 - Atkinson, Malcolm P. A1 - Dmitriev, Misha A1 - Hamilton, Craig A1 - Printezis, Tony JF - POS ER - TY - CONF T1 - Evolutionary Data Conversion in the PJama Persistent Language T2 - ECOOP Workshop on Object-Oriented Databases Y1 - 1999 A1 - Dmitriev, Misha A1 - Atkinson, Malcolm P. JF - ECOOP Workshop on Object-Oriented Databases ER - TY - CONF T1 - Evolutionary Data Conversion in the PJama Persistent Language T2 - ECOOP Workshops Y1 - 1999 A1 - Dmitriev, Misha A1 - Atkinson, Malcolm P. JF - ECOOP Workshops ER - TY - CONF T1 - Population dynamics and emerging features in AEGIS T2 - Proceedings of the Genetic and Evolutionary Computation Conference Y1 - 1999 A1 - Eiben, A. E. A1 - Elia, D. A1 - van Hemert, J. I. ED - W. Banzhaf ED - J. Daida ED - Eiben, A. E. ED - M. H. Garzon ED - V. Honavar ED - M. Jakiela ED - R. E. Smith KW - dynamic problems AB - We describe an empirical investigation within an artificial world, aegis, where a population of animals and plants is evolving. We compare different system setups in search of an `ideal' world that allows a constantly high number of inhabitants for a long period of time. We observe that high responsiveness at individual level (speed of movement) or population level (high fertility) are `ideal'. Furthermore, we investigate the emergence of the so-called mental features of animals determining their social, consumptional and aggressive behaviour. The tests show that being socially oriented is generally advantageous, while agressive behaviour only emerges under specific circumstances. JF - Proceedings of the Genetic and Evolutionary Computation Conference PB - Morgan Kaufmann Publishers, San Francisco ER - TY - CHAP T1 - SAW-ing EAs: adapting the fitness function for solving constrained problems T2 - New ideas in optimization Y1 - 1999 A1 - Eiben, A. E. A1 - van Hemert, J. I. ED - D. Corne ED - M. Dorigo ED - F. Glover KW - constraint satisfaction AB - In this chapter we describe a problem independent method for treating constrain ts in an evolutionary algorithm. Technically, this method amounts to changing the defini tion of the fitness function during a run of an EA, based on feedback from the search pr ocess. Obviously, redefining the fitness function means redefining the problem to be sol ved. On the short term this deceives the algorithm making the fitness values deteriorate , but as experiments clearly indicate, on the long run it is beneficial. We illustrate t he power of the method on different constraint satisfaction problems and point out other application areas of this technique. JF - New ideas in optimization PB - McGraw-Hill, London ER -