TY - CONF T1 - Towards Addressing CPU-Intensive Seismological Applications in Europe T2 - International Supercomputing Conference Y1 - 2013 A1 - Michele Carpené A1 - I.A. Klampanos A1 - Siew Hoon Leong A1 - Emanuele Casarotti A1 - Peter Danecek A1 - Graziella Ferini A1 - Andre Gemünd A1 - Amrey Krause A1 - Lion Krischer A1 - Federica Magnoni A1 - Marek Simon A1 - Alessandro Spinuso A1 - Luca Trani A1 - Malcolm Atkinson A1 - Giovanni Erbacci A1 - Anton Frank A1 - Heiner Igel A1 - Andreas Rietbrock A1 - Horst Schwichtenberg A1 - Jean-Pierre Vilotte AB - Advanced application environments for seismic analysis help geoscientists to execute complex simulations to predict the behaviour of a geophysical system and potential surface observations. At the same time data collected from seismic stations must be processed comparing recorded signals with predictions. The EU-funded project VERCE (http://verce.eu/) aims to enable specific seismological use-cases and, on the basis of requirements elicited from the seismology community, provide a service-oriented infrastructure to deal with such challenges. In this paper we present VERCE’s architecture, in particular relating to forward and inverse modelling of Earth models and how the, largely file-based, HPC model can be combined with data streaming operations to enhance the scalability of experiments.We posit that the integration of services and HPC resources in an open, collaborative environment is an essential medium for the advancement of sciences of critical importance, such as seismology. JF - International Supercomputing Conference CY - Leipzig, Germany ER - TY - CONF T1 - Towards automatic detection of abnormal retinal capillaries in ultra-widefield-of-view retinal angiographic exams T2 - Conf Proc IEEE Eng Med Biol Soc Y1 - 2013 A1 - Zutis, K. A1 - Trucco, E. A1 - Hubschman, J. P. A1 - Reed, D. A1 - Shah, S. A1 - van Hemert, J. KW - retinal imaging AB - Retinal capillary abnormalities include small, leaky, severely tortuous blood vessels that are associated with a variety of retinal pathologies. We present a prototype image-processing system for detecting abnormal retinal capillary regions in ultra-widefield-of-view (UWFOV) fluorescein angiography exams of the human retina. The algorithm takes as input an UWFOV FA frame and returns the candidate regions identified. An SVM classifier is trained on regions traced by expert ophthalmologists. Tests with a variety of feature sets indicate that edge features and allied properties differentiate best between normal and abnormal retinal capillary regions. Experiments with an initial set of images from patients showing branch retinal vein occlusion (BRVO) indicate promising area under the ROC curve of 0.950 and a weighted Cohen's Kappa value of 0.822. JF - Conf Proc IEEE Eng Med Biol Soc ER - TY - CONF T1 - TOPP goes Rapid T2 - Cluster Computing and the Grid, IEEE International Symposium on Y1 - 2010 A1 - Gesing, Sandra A1 - van Hemert, Jano A1 - Jos Koetsier A1 - Bertsch, Andreas A1 - Kohlbacher, Oliver AB - Proteomics, the study of all the proteins contained in a particular sample, e.g., a cell, is a key technology in current biomedical research. The complexity and volume of proteomics data sets produced by mass spectrometric methods clearly suggests the use of grid-based high-performance computing for analysis. TOPP and OpenMS are open-source packages for proteomics data analysis; however, they do not provide support for Grid computing. In this work we present a portal interface for high-throughput data analysis with TOPP. The portal is based on Rapid, a tool for efficiently generating standardized portlets for a wide range of applications. The web-based interface allows the creation and editing of user-defined pipelines and their execution and monitoring on a Grid infrastructure. The portal also supports several file transfer protocols for data staging. It thus provides a simple and complete solution to high-throughput proteomics data analysis for inexperienced users through a convenient portal interface. JF - Cluster Computing and the Grid, IEEE International Symposium on PB - IEEE Computer Society CY - Los Alamitos, CA, USA SN - 978-0-7695-4039-9 ER - TY - CONF T1 - Towards Optimising Distributed Data Streaming Graphs using Parallel Streams T2 - Data Intensive Distributed Computing (DIDC'10), in conjunction with the 19th International Symposium on High Performance Distributed Computing Y1 - 2010 A1 - Chee Sun Liew A1 - Atkinson, Malcolm P. A1 - van Hemert, Jano A1 - Liangxiu Han KW - Data-intensive Computing KW - Distributed Computing KW - Optimisation KW - Parallel Stream KW - Scientific Workflows AB - Modern scientific collaborations have opened up the opportunity of solving complex problems that involve multi- disciplinary expertise and large-scale computational experiments. These experiments usually involve large amounts of data that are located in distributed data repositories running various software systems, and managed by different organisations. A common strategy to make the experiments more manageable is executing the processing steps as a workflow. In this paper, we look into the implementation of fine-grained data-flow between computational elements in a scientific workflow as streams. We model the distributed computation as a directed acyclic graph where the nodes represent the processing elements that incrementally implement specific subtasks. The processing elements are connected in a pipelined streaming manner, which allows task executions to overlap. We further optimise the execution by splitting pipelines across processes and by introducing extra parallel streams. We identify performance metrics and design a measurement tool to evaluate each enactment. We conducted ex- periments to evaluate our optimisation strategies with a real world problem in the Life Sciences—EURExpress-II. The paper presents our distributed data-handling model, the optimisation and instrumentation strategies and the evaluation experiments. We demonstrate linear speed up and argue that this use of data-streaming to enable both overlapped pipeline and parallelised enactment is a generally applicable optimisation strategy. JF - Data Intensive Distributed Computing (DIDC'10), in conjunction with the 19th International Symposium on High Performance Distributed Computing PB - ACM CY - Chicago, Illinois UR - http://www.cct.lsu.edu/~kosar/didc10/index.php ER - TY - JOUR T1 - Towards a Virtual Fly Brain JF - Philosophical Transactions A Y1 - 2009 A1 - Armstrong, J. D. A1 - van Hemert, J. I. KW - e-Science AB - Models of the brain that simulate sensory input, behavioural output and information processing in a biologically plausible manner pose significant challenges to both Computer Science and Biology. Here we investigated strategies that could be used to create a model of the insect brain, specifically that of Drosophila melanogaster which is very widely used in laboratory research. The scale of the problem is an order of magnitude above the most complex of the current simulation projects and it is further constrained by the relative sparsity of available electrophysiological recordings from the fly nervous system. However, fly brain research at the anatomical and behavioural level offers some interesting opportunities that could be exploited to create a functional simulation. We propose to exploit these strengths of Drosophila CNS research to focus on a functional model that maps biologically plausible network architecture onto phenotypic data from neuronal inhibition and stimulation studies, leaving aside biophysical modelling of individual neuronal activity for future models until more data is available. VL - 367 UR - http://rsta.royalsocietypublishing.org/content/367/1896/2387.abstract ER - TY - CONF T1 - Towards a Grid-Enabled Simulation Framework for Nano-CMOS Electronics T2 - 3rd IEEE International Conference on eScience and Grid Computing Y1 - 2007 A1 - Liangxiu Han A1 - Asen Asenov A1 - Dave Berry A1 - Campbell Millar A1 - Gareth Roy A1 - Scott Roy A1 - Richard Sinnott A1 - Gordon Stewart AB - The electronics design industry is facing major challenges as transistors continue to decrease in size. The next generation of devices will be so small that the position of individual atoms will affect their behaviour. This will cause the transistors on a chip to have highly variable characteristics, which in turn will impact circuit and system design tools. The EPSRC project “Meeting the Design Challenges of Nano-CMOS Electronics” (Nano-CMOS) has been funded to explore this area. In this paper, we describe the distributed data-management and computing framework under development within Nano-CMOS. A key aspect of this framework is the need for robust and reliable security mechanisms that support distributed electronics design groups who wish to collaborate by sharing designs, simulations, workflows, datasets and computation resources. This paper presents the system design, and an early prototype of the project which hasbeen useful in helping us to understand the benefits of such a grid infrastructure. In particular, we also present two typical use cases: user authentication, and execution of large-scale device simulations. JF - 3rd IEEE International Conference on eScience and Grid Computing PB - IEEE Computer Society CY - Bangalore, India ER - TY - CONF T1 - 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 - 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 -