TY - CONF T1 - Applying selectively parallel IO compression to parallel storage systems T2 - Euro-Par Y1 - 2014 A1 - Rosa Filgueira A1 - Malcolm Atkinson A1 - Yusuke Tanimura A1 - Isao Kojima JF - Euro-Par ER - TY - CONF T1 - FAST: Flexible Automated Syncrhonization Transfer tool T2 - Proceedings of the Sixth International Workshop on Data-Intensive Distributed Computing Date Y1 - 2014 A1 - Rosa Filgueira A1 - Iraklis Klampanos A1 - Yusuke Tanimura A1 - Malcolm Atkinson. JF - Proceedings of the Sixth International Workshop on Data-Intensive Distributed Computing Date PB - ACM CY - New York, NY, USA ER - TY - JOUR T1 - Precise montaging and metric quantification of retinal surface area from ultra-widefield fundus photography and fluorescein angiography JF - Ophthalmic Surg Lasers Imaging Retina Y1 - 2014 A1 - Croft, D.E. A1 - van Hemert, J. A1 - Wykoff, C.C. A1 - Clifton, D. A1 - Verhoek, M. A1 - Fleming, A. A1 - Brown, D.M. KW - medical KW - retinal imaging AB - BACKGROUND AND OBJECTIVE: Accurate quantification of retinal surface area from ultra-widefield (UWF) images is challenging due to warping produced when the retina is projected onto a two-dimensional plane for analysis. By accounting for this, the authors sought to precisely montage and accurately quantify retinal surface area in square millimeters. PATIENTS AND METHODS: Montages were created using Optos 200Tx (Optos, Dunfermline, U.K.) images taken at different gaze angles. A transformation projected the images to their correct location on a three-dimensional model. Area was quantified with spherical trigonometry. Warping, precision, and accuracy were assessed. RESULTS: Uncorrected, posterior pixels represented up to 79% greater surface area than peripheral pixels. Assessing precision, a standard region was quantified across 10 montages of the same eye (RSD: 0.7%; mean: 408.97 mm(2); range: 405.34-413.87 mm(2)). Assessing accuracy, 50 patients' disc areas were quantified (mean: 2.21 mm(2); SE: 0.06 mm(2)), and the results fell within the normative range. CONCLUSION: By accounting for warping inherent in UWF images, precise montaging and accurate quantification of retinal surface area in square millimeters were achieved. [Ophthalmic Surg Lasers Imaging Retina. 2014;45:312-317.]. VL - 45 ER - TY - Generic T1 - Varpy: A python library for volcanology and rock physics data analysis. EGU2014-3699 Y1 - 2014 A1 - Rosa Filgueira A1 - Malcolm Atkinson A1 - Andrew Bell A1 - Branwen Snelling ER - TY - JOUR T1 - The Cloud Paradigm Applied to e-Health JF - BMC Med. Inf. {&} Decision Making Y1 - 2013 A1 - Jordi Vilaplana A1 - Francesc Solsona A1 - Francesc Abella A1 - Rosa Filgueira A1 - Josep Rius Torrento VL - 13 ER - TY - JOUR T1 - Exploiting Parallel R in the Cloud with SPRINT JF - Methods of Information in Medicine Y1 - 2013 A1 - Piotrowski, Michal A1 - Gary McGilvary A1 - Sloan, Terence A1 - Mewissen, Muriel A1 - Ashley Lloyd A1 - Forster, Thorsten A1 - Mitchell, Lawrence A1 - Ghazal, Peter A1 - Hill, Jon AB - Background: Advances in DNA Microarray devices and next-generation massively parallel DNA sequencing platforms have led to an exponential growth in data availability but the arising opportunities require adequate computing resources. High Performance Computing (HPC) in the Cloud offers an affordable way of meeting this need. Objectives: Bioconductor, a popular tool for high-throughput genomic data analysis, is distributed as add-on modules for the R statistical programming language but R has no native capabilities for exploiting multi-processor architectures. SPRINT is an R package that enables easy access to HPC for genomics researchers. This paper investigates: setting up and running SPRINT-enabled genomic analyses on Amazon’s Elastic Compute Cloud (EC2), the advantages of submitting applications to EC2 from different parts of the world and, if resource underutilization can improve application performance. Methods: The SPRINT parallel implementations of correlation, permutation testing, partitioning around medoids and the multi-purpose papply have been benchmarked on data sets of various size on Amazon EC2. Jobs have been submitted from both the UK and Thailand to investigate monetary differences. Results: It is possible to obtain good, scalable performance but the level of improvement is dependent upon the nature of algorithm. Resource underutilization can further improve the time to result. End-user’s location impacts on costs due to factors such as local taxation. Conclusions: Although not designed to satisfy HPC requirements, Amazon EC2 and cloud computing in general provides an interesting alternative and provides new possibilities for smaller organisations with limited funds. VL - 52 IS - 1 ER - TY - CONF T1 - MPI collective I/O based on advanced reservations to obtain performance guarantees from shared storage systems T2 - CLUSTER Y1 - 2013 A1 - Yusuke Tanimura A1 - Rosa Filgueira A1 - Isao Kojima A1 - Malcolm P. Atkinson JF - CLUSTER ER - TY - CONF T1 - SANComSim: A Scalable, Adaptive and Non-intrusive Framework to Optimize Performance in Computational Science Applications T2 - ICCS Y1 - 2013 A1 - Alberto Nuñez A1 - Rosa Filgueira A1 - Mercedes G. Merayo JF - ICCS 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 - Abstract: Reservation-Based I/O Performance Guarantee for MPI-IO Applications Using Shared Storage Systems T2 - SC Companion Y1 - 2012 A1 - Yusuke Tanimura A1 - Rosa Filgueira A1 - Isao Kojima A1 - Malcolm P. Atkinson JF - SC Companion ER - TY - CONF T1 - An adaptive, scalable, and portable technique for speeding up MPI-based applications T2 - International European Conference on Parallel and Distributed Computing, Europar-2012 Y1 - 2012 A1 - Rosa Filgueira A1 - Alberto Nuñez A1 - Javier Fernandez A1 - Malcolm Atkinson JF - International European Conference on Parallel and Distributed Computing, Europar-2012 ER - TY - JOUR T1 - Consistency and repair for XML write-access control policies JF - VLDB J. Y1 - 2012 A1 - Loreto Bravo A1 - James Cheney A1 - Irini Fundulaki A1 - Ricardo Segovia VL - 21 ER - TY - JOUR T1 - Dimensioning Scientific Computing Systems to Improve Performance of Map-Reduce based Applications JF - Procedia CS Y1 - 2012 A1 - Gabriel G. Castañè A1 - Alberto Nuñez A1 - Rosa Filgueira A1 - Jesus Carretero VL - 9 ER - TY - CONF T1 - Dimensioning Scientific Computing Systems to Improve Performance of Map-Reduce based Applications T2 - Procedia Computer Science, Proceedings of the International Conference on Computational Science, ICCS 2012 Y1 - 2012 A1 - Gabriel G. Castañè A1 - Alberto Nuñez A1 - Rosa Filgueira A1 - Jesus Carretero JF - Procedia Computer Science, Proceedings of the International Conference on Computational Science, ICCS 2012 ER - TY - CONF T1 - MoSGrid: Progress of Workflow driven Chemical Simulations T2 - Grid Workflow Workshop 2011 Y1 - 2012 A1 - Birkenheuer, Georg A1 - Blunk, Dirk A1 - Breuers, Sebastian A1 - Brinkmann, André A1 - Fels, Gregor A1 - Gesing, Sandra A1 - Grunzke, Richard A1 - Herres-Pawlis, Sonja A1 - Kohlbacher, Oliver A1 - Krüger, Jens A1 - Packschies, Lars A1 - Schäfer, Patrick A1 - Schuller, B. A1 - Schuster, Johannes A1 - Steinke, Thomas A1 - Szikszay Fabri, Anna A1 - Wewior, Martin A1 - Müller-Pfefferkorn, Ralph A1 - Kohlbacher, Oliver JF - Grid Workflow Workshop 2011 PB - CEUR Workshop Proceedings ER - TY - JOUR T1 - Principles of Provenance (Dagstuhl Seminar 12091) JF - Dagstuhl Reports Y1 - 2012 A1 - James Cheney A1 - Anthony Finkelstein A1 - Bertram Ludäscher A1 - Stijn Vansummeren VL - 2 ER - TY - JOUR T1 - SIMCAN: A flexible, scalable and expandable simulation platform for modelling and simulating distributed architectures and applications JF - Simulation Modelling Practice and Theory Y1 - 2012 A1 - Alberto Nuñez A1 - Javier Fernández A1 - Rosa Filgueira A1 - Félix García Carballeira A1 - Jesús Carretero VL - 20 ER - TY - JOUR T1 - A Single Sign-On Infrastructure for Science Gateways on a Use Case for Structural Bioinformatics JF - Journal of Grid Computing Y1 - 2012 A1 - Gesing, Sandra A1 - Grunzke, Richard A1 - Krüger, Jens A1 - Birkenheuer, Georg A1 - Wewior, Martin A1 - Schäfer, Patrick A1 - Schuller, Bernd A1 - Schuster, Johannes A1 - Herres-Pawlis, Sonja A1 - Breuers, Sebastian A1 - Balaskó, Ákos A1 - Kozlovszky, Miklos A1 - Fabri, AnnaSzikszay A1 - Packschies, Lars A1 - Kacsuk, Peter A1 - Blunk, Dirk A1 - Steinke, Thomas A1 - Brinkmann, André A1 - Fels, Gregor A1 - Müller-Pfefferkorn, Ralph A1 - Jäkel, René A1 - Kohlbacher, Oliver KW - DCIs KW - Science gateway KW - security KW - Single sign-on KW - Structural bioinformatics VL - 10 UR - http://dx.doi.org/10.1007/s10723-012-9247-y ER - TY - RPRT T1 - EDIM1 Progress Report Y1 - 2011 A1 - Paul Martin A1 - Malcolm Atkinson A1 - Parsons, Mark A1 - Adam Carter A1 - Gareth Francis AB - The Edinburgh Data-Intensive Machine (EDIM1) is the product of a joint collaboration between the data-intensive group at the School of Informatics and EPCC. EDIM1 is an experimental system, offering an alternative architecture for data-intensive computation and providing a platform for evaluating tools for data-intensive research; a 120 node cluster of ‘data-bricks’ with high storage yet modest computational capacity. This document gives some background into the context in which EDIM1 was designed and constructed, as well as providing an overview of its use so far and future plans. ER - TY - CONF T1 - Granular Security for a Science Gateway in Structural Bioinformatics T2 - Proceedings of the International Workshop on Science Gateways for Life Sciences (IWSG-Life 2011) Y1 - 2011 A1 - Gesing, Sandra A1 - Grunzke, Richard A1 - Balaskó, Ákos A1 - Birkenheuer, Georg A1 - Blunk, Dirk A1 - Breuers, Sebastian A1 - Brinkmann, André A1 - Fels, Gregor A1 - Herres-Pawlis, Sonja A1 - Kacsuk, Peter A1 - Kozlovszky, Miklos A1 - Krüger, Jens A1 - Packschies, Lars A1 - Schäfer, Patrick A1 - Schuller, Bernd A1 - Schuster, Johannes A1 - Steinke, Thomas A1 - Szikszay Fabri, Anna A1 - Wewior, Martin A1 - Müller-Pfefferkorn, Ralph A1 - Kohlbacher, Oliver JF - Proceedings of the International Workshop on Science Gateways for Life Sciences (IWSG-Life 2011) PB - CEUR Workshop Proceedings ER - TY - CONF T1 - A Science Gateway for Molecular Simulations T2 - EGI User Forum 2011 Y1 - 2011 A1 - Gesing, Sandra A1 - Kacsuk, Peter A1 - Kozlovszky, Miklos A1 - Birkenheuer, Georg A1 - Blunk, Dirk A1 - Breuers, Sebastian A1 - Brinkmann, André A1 - Fels, Gregor A1 - Grunzke, Richard A1 - Herres-Pawlis, Sonja A1 - Krüger, Jens A1 - Packschies, Lars A1 - Müller-Pfefferkorn, Ralph A1 - Schäfer, Patrick A1 - Steinke, Thomas A1 - Szikszay Fabri, Anna A1 - Warzecha, Klaus A1 - Wewior, Martin A1 - Kohlbacher, Oliver JF - EGI User Forum 2011 SN - 978 90 816927 1 7 ER - TY - JOUR T1 - Adaptive CoMPI: Enhancing MPI based applications performance and scalability by using adaptive compression. JF - International Journal of High Performance Computing and Applications, 2010. Sage Y1 - 2010 A1 - Rosa Filgueira A1 - David E. Singh A1 - Alejandro Calderón A1 - Félix García Carballeira A1 - Jesús Carretero AB - This paper presents an optimization of MPI communication, called Adaptive-CoMPI, based on runtime compression of MPI messages exchanged by applications. The technique developed can be used for any application, because its implementation is transparent for the user, and integrates different compression algorithms for both MPI collective and point-to-point primitives. Furthermore, compression is turned on and off and the most appropriate compression algorithms are selected at runtime, depending on the characteristics of each message, the network behavior, and compression algorithm behavior, following a runtime adaptive strategy. Our system can be optimized for a specific application, through a guided strategy, to reduce the runtime strategy overhead. Adaptive-CoMPI has been validated using several MPI benchmarks and real HPC applications. Results show that, in most cases, by using adaptive compression, communication time is reduced, enhancing application performance and scalability. IS - 25 (3) ER - TY - JOUR T1 - Dynamic-CoMPI: Dynamic optimization techniques for MPI parallel applications. JF - The Journal of Supercomputing. Y1 - 2010 A1 - Rosa Filgueira A1 - Jesús Carretero A1 - David E. Singh A1 - Alejandro Calderón A1 - Alberto Nunez KW - Adaptive systems KW - Clusters architectures KW - Collective I/O KW - Compression algorithms KW - Heuristics KW - MPI library - Parallel techniques AB - This work presents an optimization of MPI communications, called Dynamic-CoMPI, which uses two techniques in order to reduce the impact of communications and non-contiguous I/O requests in parallel applications. These techniques are independent of the application and complementaries to each other. The first technique is an optimization of the Two-Phase collective I/O technique from ROMIO, called Locality aware strategy for Two-Phase I/O (LA-Two-Phase I/O). In order to increase the locality of the file accesses, LA-Two-Phase I/O employs the Linear Assignment Problem (LAP) for finding an optimal I/O data communication schedule. The main purpose of this technique is the reduction of the number of communications involved in the I/O collective operation. The second technique, called Adaptive-CoMPI, is based on run-time compression of MPI messages exchanged by applications. Both techniques can be applied on every application, because both of them are transparent for the users. Dynamic-CoMPI has been validated by using several MPI benchmarks and real HPC applications. The results show that, for many of the considered scenarios, important reductions in the execution time are achieved by reducing the size and the number of the messages. Additional benefits of our approach are the reduction of the total communication time and the network contention, thus enhancing, not only performance, but also scalability. PB - Springer ER - TY - CONF T1 - Grid-Workflows in Molecular Science T2 - Software Engineering 2010, Grid Workflow Workshop Y1 - 2010 A1 - Birkenheuer, Georg A1 - Breuers, Sebastian A1 - Brinkmann, André A1 - Blunk, Dirk A1 - Fels, Gregor A1 - Gesing, Sandra A1 - Herres-Pawlis, Sonja A1 - Kohlbacher, Oliver A1 - Krüger, Jens A1 - Packschies, Lars JF - Software Engineering 2010, Grid Workflow Workshop PB - GI-Edition - Lecture Notes in Informatics (LNI) ER - TY - CONF T1 - Workflow Interoperability in a Grid Portal for Molecular Simulations T2 - Proceedings of the International Workshop on Science Gateways (IWSG10) Y1 - 2010 A1 - Gesing, Sandra A1 - Marton, Istvan A1 - Birkenheuer, Georg A1 - Schuller, Bernd A1 - Grunzke, Richard A1 - Krüger, Jens A1 - Breuers, Sebastian A1 - Blunk, Dirk A1 - Fels, Gregor A1 - Packschies, Lars A1 - Brinkmann, André A1 - Kohlbacher, Oliver A1 - Kozlovszky, Miklos JF - Proceedings of the International Workshop on Science Gateways (IWSG10) PB - Consorzio COMETA ER - TY - CONF T1 - Adoption of e-Infrastructure Services: inhibitors, enablers and opportunities T2 - 5th International Conference on e-Social Science Y1 - 2009 A1 - Voss, A. A1 - Asgari-Targhi, M. A1 - Procter, R. A1 - Halfpenny, P. A1 - Fragkouli, E. A1 - Anderson, S. A1 - Hughes, L. A1 - Fergusson, D. A1 - Vander Meer, E. A1 - Atkinson, M. AB - Based on more than 100 interviews with respondents from the academic community and information services, we present findings from our study of inhibitors and enablers of adoption of e-Infrastructure services for research. We discuss issues raised and potential ways of addressing them. JF - 5th International Conference on e-Social Science CY - Maternushaus, Cologne ER - TY - CONF T1 - CoMPI: Enhancing MPI Based Applications Performance and Scalability Using Run-Time Compression. T2 - EUROPVM/MPI 2009.Espoo, Finland. September 2009 Y1 - 2009 A1 - Rosa Filgueira A1 - David E. Singh A1 - Alejandro Calderón A1 - Jesús Carretero AB - This paper presents an optimization of MPI communications, called CoMPI, based on run-time compression of MPI messages exchanged by applications. A broad number of compression algorithms have been fully implemented and tested for both MPI collective and point to point primitives. In addition, this paper presents a study of several compression algorithms that can be used for run-time compression, based on the datatype used by applications. This study has been validated by using several MPI benchmarks and real HPC applications. Show that, in most of the cases, using compression reduces the application communication time enhancing application performance and scalability. In this way, CoMPI obtains important improvements in the overall execution time for many of the considered scenarios. JF - EUROPVM/MPI 2009.Espoo, Finland. September 2009 PB - Springer CY - Espoo. Finland VL - 5759/2009 ER - TY - JOUR T1 - 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 - CONF T1 - Using architectural simulation models to aid the design of data intensive application T2 - The Third International Conference on Advanced Engineering Computing and Applications in Sciences (ADVCOMP 2009) Y1 - 2009 A1 - Javier Fernández A1 - Liangxiu Han A1 - Alberto Nuñez A1 - Jesus Carretero A1 - van Hemert, Jano JF - The Third International Conference on Advanced Engineering Computing and Applications in Sciences (ADVCOMP 2009) PB - IEEE Computer Society CY - Sliema, Malta ER - TY - CONF T1 - Data Locality Aware Strategy for Two-Phase Collective I/O T2 - VECPAR Y1 - 2008 A1 - Rosa Filgueira A1 - David E. Singh A1 - Juan Carlos Pichel A1 - Florin Isaila A1 - Jesús Carretero JF - VECPAR ER - TY - JOUR T1 - Distributed Computing Education, Part 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 3: The Winter School Online Experience JF - Distributed Systems Online Y1 - 2008 A1 - Low, B. A1 - Cassidy, K. A1 - Fergusson, D. A1 - Atkinson, M. A1 - Vander Meer, E. A1 - McGeever, M. AB - The International Summer Schools in Grid Computing (ISSGC) have provided numerous international students with the opportunity to learn grid systems, as detailed in part 2 of this series (http://doi.ieeecomputersociety.org/10.1109/MDSO.2008.20). The International Winter School on Grid Computing 2008 (IWSGC 08) followed the successful summer schools, opening up the ISSGC experience to a wider range of students because of its online format. The previous summer schools made it clear that many students found the registration and travel costs and the time requirements prohibitive. The EU FP6 ICEAGE project held the first winter school from 6 February to 12 March 2008. The winter school repurposed summer school materials and added resources such as the ICEAGE digital library and summer-school-tested t-Infrastructures such as GILDA (Grid INFN Laboratory for Dissemination Activities). The winter schools shared the goals of the summer school, which emphasized disseminating grid knowledge. The students act as multipliers, spreading the skills and knowledge they acquired at the winter school to their colleagues to build strong and enthusiastic local grid communities. PB - IEEE Computer Society VL - 9 UR - http://ieeexplore.ieee.org/stamp/stamp.jsp?tp=&arnumber=4659260 IS - 9 ER - TY - JOUR T1 - Distributed Computing Education, Part 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 - JOUR T1 - Distributed Computing Education, Part 5: Coming to Terms with Intellectual Property Rights JF - Distributed Systems Online Y1 - 2008 A1 - Boon Low A1 - Kathryn Cassidy A1 - Fergusson, David A1 - Malcolm Atkinson A1 - Elizabeth Vander Meer A1 - Mags McGeever AB - In part 1 of this series on distributed computing education, we introduced a list of components important for teaching environments. We outlined the first three components, which included development of materials for education, education for educators and teaching infrastructures, identifying current practice, challenges, and opportunities for provision. The final component, a supportive policy framework that encourages cooperation and sharing, includes the need to manage intellectual property rights (IPR). PB - IEEE Computer Society VL - 9 UR - http://ieeexplore.ieee.org/stamp/stamp.jsp?tp=&arnumber=4755177 IS - 12 ER - TY - RPRT T1 - Education and Training Task Force Report Y1 - 2008 A1 - Atkinson, M. A1 - Vander Meer, E. A1 - Fergusson, D. A1 - Artacho, M. AB - The development of e-Infrastructure, of which grid computing is a fundamental element, will have major economic and social benefits. Online and financial businesses already successfully use grid computing technologies, for instance. There are already demonstrations showing the benefits to engineering, medicine and the creative industries as well. New research methods and technologies generate large data sets that need to be shared in order to ensure continued social and scientific research and innovation. e-Infrastructure provides an environment for coping with these large data sets and for sharing data across regions. An investment in educating people in this technology, then, is an investment that will strengthen our economies and societies. In order to deliver e-Infrastructure education and training successfully in the EU, we must develop a policy framework that will ensure shared responsibility and equivalent training in the field. This document focuses primarily on the current state of grid and e-Science education, introducing key challenges and the opportunities available to educational planners that serve as a starting point for further work. It then proposes strategies and policies to provide a supportive framework for e-Infrastructure education and training. The ETTF Report concludes with policy recommendations to be taken forward by the e-IRG. These recommendations address issues such as the level of Member State investment in e-Infrastructure education, the harmonisation of education in distributed-computation thinking and in the use of e-Infrastructure and the development of standards for student and teacher identification, for the sharing of t-Infrastructure (and training material) and for accreditation. JF - e-Infrastructure Reflection Group UR - http://www.e-irg.eu/index.php?option=com_content&task=view&id=38&Itemid=37 ER - TY - CONF T1 - Exploiting data compression in collective I/O techniques. T2 - Cluster Computing 2008. Y1 - 2008 A1 - Rosa Filgueira A1 - David E. Singh A1 - Juan Carlos Pichel A1 - Jesús Carretero JF - Cluster Computing 2008. CY - Tsukuba, Japand. SN - 978-1-4244-2639-3 ER - TY - CONF T1 - 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 - 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 - 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 - Optimization and evaluation of parallel I/O in BIPS3D parallel irregular application T2 - IPDPS Y1 - 2007 A1 - Rosa Filgueira A1 - David E. Singh A1 - Florin Isaila A1 - Jesús Carretero A1 - Antonio Garcia Loureiro JF - IPDPS ER - TY - CONF T1 - EGEE: building a pan-European grid training organisation T2 - ACSW Frontiers Y1 - 2006 A1 - Berlich, R{\"u}diger A1 - Hardt, Marcus A1 - Kunze, Marcel A1 - Atkinson, Malcolm P. A1 - Fergusson, David JF - ACSW Frontiers 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 - Organization of the International Testbed of the CrossGrid Project T2 - Cracow Grid Workshop 2005 Y1 - 2005 A1 - Gomes, J. A1 - David, M. A1 - Martins, J. A1 - Bernardo, L. A1 - Garcia, A. A1 - Hardt, M. A1 - Kornmayer, H. A1 - Marco, Rafael A1 - Rodríguez, David A1 - Diaz, Irma A1 - Cano, Daniel A1 - Salt, J. A1 - Gonzalez, S. A1 - Sanchez, J. A1 - Fassi, F. A1 - Lara, V. A1 - Nyczyk, P. A1 - Lason, P. A1 - Ozieblo, A. A1 - Wolniewicz, P. A1 - Bluj, M. JF - Cracow Grid Workshop 2005 ER - TY - JOUR T1 - Specifying use case behavior with interaction models JF - Journal of Object Technology Y1 - 2005 A1 - José Daniel Garcia A1 - Jesús Carretero A1 - José Maria Pérez A1 - Félix García Carballeira A1 - Rosa Filgueira VL - 4 ER - TY - 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 - Development of a Grid Infrastructure for Functional Genomics T2 - Life Science Grid Conference (LSGrid 2004) Y1 - 2004 A1 - Sinnott, R. O. A1 - Bayer, M. A1 - Houghton, D. A1 - D. Berry A1 - Ferrier, M. JF - Life Science Grid Conference (LSGrid 2004) T3 - LNCS PB - Springer Verlag CY - Kanazawa, Japan ER - TY - 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 - 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 - 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 - CHAP T1 - Data Access, Integration, and Management T2 - The Grid 2: Blueprint for a New Computing Infrastructure (2nd edition), Y1 - 2003 A1 - Atkinson. M. A1 - Chervenak, A. L. A1 - Kunszt, P. A1 - Narang, I. A1 - Paton, N. W. A1 - Pearson, D. A1 - Shoshani, A. A1 - Watson, P. ED - Foster, I. ED - Kesselman, C JF - The Grid 2: Blueprint for a New Computing Infrastructure (2nd edition), PB - Morgan Kaufmann SN - 1-55860-933-4 ER - TY - CHAP T1 - Rationale for Choosing the Open Grid Services Architecture T2 - Grid Computing: Making the Global Infrastructure a Reality Y1 - 2003 A1 - Atkinson, M. ED - F. Berman ED - G. Fox ED - T. Hey JF - Grid Computing: Making the Global Infrastructure a Reality PB - John Wiley & Sons, Ltd CY - Chichester, UK SN - 9780470853191 ER - TY - CONF T1 - Measuring the Searched Space to Guide Efficiency: The Principle and Evidence on Constraint Satisfaction T2 - Springer Lecture Notes on Computer Science Y1 - 2002 A1 - van Hemert, J. I. A1 - Bäck, T. ED - J. J. Merelo ED - A. Panagiotis ED - H.-G. Beyer ED - Jos{\'e}-Luis Fern{\'a}ndez-Villaca{\~n}as ED - Hans-Paul Schwefel KW - constraint satisfaction KW - resampling ratio AB - In this paper we present a new tool to measure the efficiency of evolutionary algorithms by storing the whole searched space of a run, a process whereby we gain insight into the number of distinct points in the state space an algorithm has visited as opposed to the number of function evaluations done within the run. This investigation demonstrates a certain inefficiency of the classical mutation operator with mutation-rate 1/l, where l is the dimension of the state space. Furthermore we present a model for predicting this inefficiency and verify it empirically using the new tool on binary constraint satisfaction problems. JF - Springer Lecture Notes on Computer Science PB - Springer-Verlag, Berlin SN - 3-540-44139-5 ER - TY - CONF T1 - Adapting the Fitness Function in GP for Data Mining T2 - Springer Lecture Notes on Computer Science Y1 - 1999 A1 - Eggermont, J. A1 - Eiben, A. E. A1 - van Hemert, J. I. ED - R. Poli ED - P. Nordin ED - W. B. Langdon ED - T. C. Fogarty KW - data mining KW - genetic programming AB - In this paper we describe how the Stepwise Adaptation of Weights (SAW) technique can be applied in genetic programming. The SAW-ing mechanism has been originally developed for and successfully used in EAs for constraint satisfaction problems. Here we identify the very basic underlying ideas behind SAW-ing and point out how it can be used for different types of problems. In particular, SAW-ing is well suited for data mining tasks where the fitness of a candidate solution is composed by `local scores' on data records. We evaluate the power of the SAW-ing mechanism on a number of benchmark classification data sets. The results indicate that extending the GP with the SAW-ing feature increases its performance when different types of misclassifications are not weighted differently, but leads to worse results when they are. JF - Springer Lecture Notes on Computer Science PB - Springer-Verlag, Berlin SN - 3-540-65899-8 ER -