TY - CONF T1 - Automatic Extraction of the Optic Disc Boundary for Detecting Retinal Diseases T2 - 14th {IASTED} International Conference on Computer Graphics and Imaging (CGIM) Y1 - 2013 A1 - M.S. Haleem A1 - L. Han A1 - B. Li A1 - A. Nisbet A1 - van Hemert, J. A1 - M. Verhoek ED - L. Linsen ED - M. Kampel KW - retinal imaging AB - In this paper, we propose an algorithm based on active shape model for the extraction of Optic Disc boundary. The determination of Optic Disc boundary is fundamental to the automation of retinal eye disease diagnosis because the Optic Disc Center is typically used as a reference point to locate other retinal structures, and any structural change in Optic Disc, whether textural or geometrical, can be used to determine the occurrence of retinal diseases such as Glaucoma. The algorithm is based on determining a model for the Optic Disc boundary by learning patterns of variability from a training set of annotated Optic Discs. The model can be deformed so as to reflect the boundary of Optic Disc in any feasible shape. The algorithm provides some initial steps towards automation of the diagnostic process for retinal eye disease in order that more patients can be screened with consistent diagnoses. The overall accuracy of the algorithm was 92% on a set of 110 images. JF - 14th {IASTED} International Conference on Computer Graphics and Imaging (CGIM) PB - {ACTA} Press 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 - 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 - 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 - 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 - CHAP T1 - Multi-agent Negotiation of Virtual Machine Migration Using the Lightweight Coordination Calculus T2 - Agent and Multi-Agent Systems. Technologies and Applications Y1 - 2012 A1 - Anderson, Paul A1 - Shahriar Bijani A1 - Vichos, Alexandros ED - Jezic, Gordan ED - Kusek, Mario ED - Nguyen, Ngoc-Thanh ED - Howlett, Robert ED - Jain, Lakhmi JF - Agent and Multi-Agent Systems. Technologies and Applications T3 - Lecture Notes in Computer Science PB - Springer Berlin / Heidelberg VL - 7327 SN - 978-3-642-30946-5 UR - http://dx.doi.org/10.1007/978-3-642-30947-2_16 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 user-friendly web portal for T-Coffee on supercomputers JF - BMC Bioinformatics Y1 - 2011 A1 - J. Rius A1 - F. Cores A1 - F. Solsona A1 - van Hemert, J. I. A1 - Koetsier, J. A1 - C. Notredame KW - e-Science KW - portal KW - rapid AB - Background Parallel T-Coffee (PTC) was the first parallel implementation of the T-Coffee multiple sequence alignment tool. It is based on MPI and RMA mechanisms. Its purpose is to reduce the execution time of the large-scale sequence alignments. It can be run on distributed memory clusters allowing users to align data sets consisting of hundreds of proteins within a reasonable time. However, most of the potential users of this tool are not familiar with the use of grids or supercomputers. Results In this paper we show how PTC can be easily deployed and controlled on a super computer architecture using a web portal developed using Rapid. Rapid is a tool for efficiently generating standardized portlets for a wide range of applications and the approach described here is generic enough to be applied to other applications, or to deploy PTC on different HPC environments. Conclusions The PTC portal allows users to upload a large number of sequences to be aligned by the parallel version of TC that cannot be aligned by a single machine due to memory and execution time constraints. The web portal provides a user-friendly solution. VL - 12 UR - http://www.biomedcentral.com/1471-2105/12/150 ER - TY - JOUR T1 - 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 - 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 - Study of User Priorities for e-Infrastructure for e-Research (SUPER) T2 - Proceedings of the UK e-Science All Hands Meeting Y1 - 2007 A1 - Newhouse, S. A1 - Schopf, J. M. A1 - Richards, A. A1 - Atkinson, M. P. JF - Proceedings of the UK e-Science All Hands Meeting ER - TY - 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 - Web Service Grids: an evolutionary approach JF - Concurrency - Practice and Experience Y1 - 2005 A1 - Atkinson, Malcolm P. A1 - Roure, David De A1 - Dunlop, Alistair N. A1 - Fox, Geoffrey A1 - Henderson, Peter A1 - Hey, Anthony J. G. A1 - Paton, Norman W. A1 - Newhouse, Steven A1 - Parastatidis, Savas A1 - Trefethen, Anne E. A1 - Watson, Paul A1 - Webber, Jim VL - 17 ER - TY - CONF T1 - Dynamic Routing Problems with Fruitful Regions: Models and Evolutionary Computation T2 - LNCS Y1 - 2004 A1 - van Hemert, J. I. A1 - la Poutré, J. A. ED - Xin Yao ED - Edmund Burke ED - Jose A. Lozano ED - Jim Smith ED - Juan J. Merelo-Guerv\'os ED - John A. Bullinaria ED - Jonathan Rowe ED - Peter Ti\v{n}o Ata Kab\'an ED - Hans-Paul Schwefel KW - dynamic problems KW - evolutionary computation KW - vehicle routing AB - We introduce the concept of fruitful regions in a dynamic routing context: regions that have a high potential of generating loads to be transported. The objective is to maximise the number of loads transported, while keeping to capacity and time constraints. Loads arrive while the problem is being solved, which makes it a real-time routing problem. The solver is a self-adaptive evolutionary algorithm that ensures feasible solutions at all times. We investigate under what conditions the exploration of fruitful regions improves the effectiveness of the evolutionary algorithm. JF - LNCS PB - Springer-Verlag CY - Birmingham, UK VL - 3242 SN - 3-540-23092-0 ER - TY - CONF T1 - 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 - CONF T1 - Phase transition properties of clustered travelling salesman problem instances generated with evolutionary computation T2 - LNCS Y1 - 2004 A1 - van Hemert, J. I. A1 - Urquhart, N. B. ED - Xin Yao ED - Edmund Burke ED - Jose A. Lozano ED - Jim Smith ED - Juan J. Merelo-Guerv\'os ED - John A. Bullinaria ED - Jonathan Rowe ED - Peter Ti\v{n}o Ata Kab\'an ED - Hans-Paul Schwefel KW - evolutionary computation KW - problem evolving KW - travelling salesman AB - This paper introduces a generator that creates problem instances for the Euclidean symmetric travelling salesman problem. To fit real world problems, we look at maps consisting of clustered nodes. Uniform random sampling methods do not result in maps where the nodes are spread out to form identifiable clusters. To improve upon this, we propose an evolutionary algorithm that uses the layout of nodes on a map as its genotype. By optimising the spread until a set of constraints is satisfied, we are able to produce better clustered maps, in a more robust way. When varying the number of clusters in these maps and, when solving the Euclidean symmetric travelling salesman person using Chained Lin-Kernighan, we observe a phase transition in the form of an easy-hard-easy pattern. JF - LNCS PB - Springer-Verlag CY - Birmingham, UK VL - 3242 SN - 3-540-23092-0 UR - http://www.vanhemert.co.uk/files/clustered-phase-transition-tsp.tar.gz ER - TY - 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 - CONF T1 - Experiences of Designing and Implementing Grid Database Services in the OGSA-DAI project T2 - Global Grid Forum Workshop on Designing and Building Grid Services/GGF9 Y1 - 2003 A1 - Antonioletti, Mario A1 - Neil Chue Hong A1 - Ally Hume A1 - Mike Jackson A1 - Krause, Amy A1 - Jeremy Nowell A1 - Charaka Palansuriya A1 - Tom Sugden A1 - Martin Westhead AB - This paper describes the experiences of the OGSA-DAI team in designing and building a database access layer using the OGSI and the emerging DAIS GGF recommendations. This middleware is designed for enabling other UK e-Science projects that require database access and providing the basic primitives for higher-level services such as Distributed Query Processing. OGSA-DAI also intends to produce one of the required reference implementations of the DAIS specification once this becomes a proposed recommendation and, until then, scope out their ideas, provide feedback as well as directly contributing to the GGF working group. This paper enumerates the issues that have arisen in tracking the DAIS and OGSI specifications whilst developing a software distribution using the Grid services model; trying to serve the needs of the various target communities; and using the Globus Toolkit OGSI core distribution. The OGSA-DAI software distribution and more details are available from the project web site at http://www.ogsadai.org.uk/. JF - Global Grid Forum Workshop on Designing and Building Grid Services/GGF9 CY - Chicago, USA ER - TY - RPRT T1 - Grid Database Access and Integration: Requirements and Functionalities Y1 - 2003 A1 - Atkinson, M. P. A1 - Dialani, V. A1 - Guy, L. A1 - Narang, I. A1 - Paton, N. W. A1 - Pearson, D. A1 - Storey, T. A1 - Watson, P. AB - This document is intended to provide the context for developing Grid data service standard recommendations within the Global Grid Forum. It defines the generic requirements for accessing and integrating persistent structured and semi-structured data. In addition, it defines the generic functionalities which a Grid data service needs to provide in supporting discovery of and controlled access to data, in performing data manipulation operations, and in virtualising data resources. The document also defines the scope of Grid data service standard recommendations which are presented in a separate document. JF - Global Grid Forum ER - TY - CONF T1 - 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 -