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e-Science Workshops, 2010 Sixth IEEE International Conference on

Date 7-10 Dec. 2010

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  • [Front cover]

    Publication Year: 2010 , Page(s): C1
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  • [Title page i]

    Publication Year: 2010 , Page(s): i
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  • [Title page iii]

    Publication Year: 2010 , Page(s): iii
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  • [Copyright notice]

    Publication Year: 2010 , Page(s): iv
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  • Table of contents

    Publication Year: 2010 , Page(s): v - vii
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  • Message from the Workshop Chair

    Publication Year: 2010 , Page(s): viii
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  • e-Science Challenges in Astronomy and Astrophysics

    Publication Year: 2010 , Page(s): ix
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  • Computational Science and Engineering Workshop

    Publication Year: 2010 , Page(s): x
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  • High-Performance Computing in the Life Sciences

    Publication Year: 2010 , Page(s): xi
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  • Parallel Optimisation and Parameter Fitting

    Publication Year: 2010 , Page(s): xii
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  • Public Access to Data and the Use of Web-Enabled Tools

    Publication Year: 2010 , Page(s): xiii
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  • list-reviewer

    Publication Year: 2010 , Page(s): xiv - xv
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  • The Application of Cloud Computing to Astronomy: A Study of Cost and Performance

    Publication Year: 2010 , Page(s): 1 - 7
    Cited by:  Papers (2)
    Save to Project icon | Request Permissions | Click to expandQuick Abstract | PDF file iconPDF (337 KB) |  | HTML iconHTML  

    Cloud computing is a powerful new technology that is widely used in the business world. Recently, we have been investigating the benefits it offers to scientific computing. We have used three workflow applications to compare the performance of processing data on the Amazon EC2 cloud with the performance on the Abe high-performance cluster at the National Center for Supercomputing Applications (NCSA). We show that the Amazon EC2 cloud offers better performance and value for processor- and memory-limited applications than for I/O-bound applications. We provide an example of how the cloud is well suited to the generation of a science product: an atlas of period grams for the 210,000 light curves released by the NASA Kepler Mission. This atlas will support the identification of periodic signals, including those due to transiting exoplanets, in the Kepler data sets. View full abstract»

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  • Federating Access to Small-aperture Telescopes

    Publication Year: 2010 , Page(s): 8 - 14
    Save to Project icon | Request Permissions | Click to expandQuick Abstract | PDF file iconPDF (177 KB) |  | HTML iconHTML  

    For approximately the last four years, a system which provides for the control and efficient use of small-aperture remote and robotic telescopes has been in operation. Allowing telescopes to be made available to large numbers of people, this system is in the process of being federated and will join the Australian Access Federation (AAF). When this process is complete, member telescopes will be readily available to staff and students of institutions federated with the AAF. The telescope control system is described in detail, and the benefits of a federated approach discussed. View full abstract»

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  • Visualisation and Analysis Challenges for WALLABY

    Publication Year: 2010 , Page(s): 15 - 20
    Cited by:  Papers (1)
    Save to Project icon | Request Permissions | Click to expandQuick Abstract | PDF file iconPDF (265 KB) |  | HTML iconHTML  

    Visualisation and analysis of terabyte-scale datacubes, as will be produced with the Australian Square Kilometre Array Pathfinder (ASKAP), will pose challenges for existing astronomy software and the work practices of astronomers. Focusing on the proposed outcomes of WALLABY (Wide field ASKAP L-Band Legacy All-Sky Blind Survey), and using lessons learnt from HIPASS (HI Parkes All Sky Survey), we identify issues that astronomers will face with WALLABY data cubes. We comment on potential research directions and possible solutions to these challenges. View full abstract»

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  • Data Challenges for Next-generation Radio Telescopes

    Publication Year: 2010 , Page(s): 21 - 24
    Cited by:  Papers (2)
    Save to Project icon | Request Permissions | Click to expandQuick Abstract | PDF file iconPDF (8295 KB) |  | HTML iconHTML  

    Radio-astronomy is about to embark on a new way of doing science. The revolution that is about to take place is not due to the enormous sensitivity of the Square Kilometre Array, which is still a decade away, but due to its pathfinders, which are pioneering new ways of doing radio-astronomy. These new ways include multi-pixel phased-array feeds, the goal of producing science-ready images from a real-time pipeline processor, and from the vast amounts of survey data that will be available in the public domain soon after observing. Here I review the data challenges that need to be addressed if we are to reap all the science that potentially resides in SKA Pathfinder data. Some challenges are obvious, such as petabytes of data storage, and some are less obvious, such as the techniques we have yet to develop to perform cross-identifications on millions of galaxies. View full abstract»

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  • Application of the OpenCL API for Implementation of the NIPALS Algorithm for Principal Component Analysis of Large Data Sets

    Publication Year: 2010 , Page(s): 25 - 30
    Cited by:  Papers (1)
    Save to Project icon | Request Permissions | Click to expandQuick Abstract | PDF file iconPDF (694 KB) |  | HTML iconHTML  

    An implementation of the nonlinear iterative partial least squares algorithm (NIPALS) was used as a test case for use of OpenCL for computation on a general purpose graphics processing unit (GPGPU) cluster using MPI. Timing results are shown along with results of a model of time required per iteration for defined problem sizes. Various steps in optimization of the code are discussed, moving from use of a single GPU, to multiple GPUs on a single node, to multiple GPUs on multiple nodes. Comparison of performance between OpenCL and BLAS implementations, modern CPU architectures and NVidia Tesla and Fermi class GPU systems are given. View full abstract»

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  • A JEE-based Architecture for Distributed Multi-Domain Resource Accounting

    Publication Year: 2010 , Page(s): 31 - 38
    Save to Project icon | Request Permissions | Click to expandQuick Abstract | PDF file iconPDF (368 KB) |  | HTML iconHTML  

    Many different accounting systems currently exist for the European Grids and for other distributed systems in general. Even though they often share equivalent technical approaches, concerning accounting metrics and batch-system log access, there are lots of different data formats, accounting-database layouts, communication- and implementation details that hinder a consistent and comprehensive accounting of distributed resources. An eventual technical convergency is even more required, as the National Grid Initiatives move forward to constitute a European Grid that comprises the national infrastructures. We present EEGAS, a Java Enterprise based grid accounting system, that addresses the current problems. Our system makes use of standard building blocks, where possible, to achieve high scalability and application server console-based configurability. It serves as an integration point for existing accounting systems and uses the OGF-UR data format, which we use to generate a Java domain model and a database schema. We also present sensor components for CPU and storage accounting, resource capacity discovery, as well as different message- and service-based transport components that support a fault-tolerant operation of a distributed accounting network that features different administrative domains rather than a single centralized accounting authority. View full abstract»

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  • Haemodynamic Effect of Coronary Angulations on Subsequent Development of Coronary Artery Disease: A Preliminary Study

    Publication Year: 2010 , Page(s): 39 - 43
    Save to Project icon | Request Permissions | Click to expandQuick Abstract | PDF file iconPDF (2517 KB) |  | HTML iconHTML  

    The aim of this study is to investigate the hemodynamic effect of the angulations in the left coronary bifurcation on subsequent development of coronary artery disease. Eight 3D left coronary artery models were generated based on the anatomical details and simulated for numerical analysis. The angulations at the left coronary bifurcation were simulated with angles ranging from 120°, 105°, 90°, 75°, 60°, 45°, 30° to 15°. Computational fluid dynamic models were produced for analysis of flow velocity, wall pressure and wall shear stress. Our results showed that wide angled models produced low wall shear stress and high wall pressure at the left coronary bifurcation regions, whereas, flow pattern was more smooth and laminar with narrow angled models than those with wide angle models. Our analysis indicates the flow-field correlation between coronary angulation and development of atherosclerosis. Future studies are required to analyse the realistic coronary models from patients' data with different degree of coronary stenosis. View full abstract»

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  • Large Scale Atomistic Simulation with Electrostatics: The Case of Cation Impurity Segregation Along an Edge Dislocation Line

    Publication Year: 2010 , Page(s): 44 - 48
    Save to Project icon | Request Permissions | Click to expandQuick Abstract | PDF file iconPDF (813 KB) |  | HTML iconHTML  

    The movement of impurities and point defects in materials plays a key role in determining their rheological properties, both by permitting diffusional creep and by allowing recovery by dislocation climb. Impurity and point defect diffusion can also control the kinetics of phase transitions and grain growth, and can determine the rate of chemical equilibration between phases. Thus the study of point defects and their migration has been of considerable interest. So far, studies using computer simulation methods have concentrated on point defects moving through otherwise perfect crystals. Here, we report calculations on the behavior of the isovalent substitutional cation impurities, Ca and Sr, close to the core of an 1/2 <;110>; {11̅0} edge dislocation in MgO. By mapping the distribution of energies for impurities and point defects around the dislocation line, we reveal that the impurities are segregated towards and trapped inside the MgO edge dislocation core. In addition, Mg vacancies will strongly partition to the impurity bearing dislocation. We also find that the presence of impurities slightly increases the Mg migration activation energy. However, impurity migration in the dislocation core is substantially enhanced compared to migration through the dislocation-free crystal structure. Activation energies are 0.76-0.86 of the barrier in the perfect crystal, demonstrating the importance of pipe diffusion along extended defects for low temperature mobility in ionic materials. View full abstract»

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  • Extending the Data Model for Data-Centric Metagenomics Analysis Using Scientific Workflows in CAMERA

    Publication Year: 2010 , Page(s): 49 - 56
    Save to Project icon | Request Permissions | Click to expandQuick Abstract | PDF file iconPDF (1391 KB) |  | HTML iconHTML  

    Community Cyber infrastructure for Advanced Marine Microbial Ecology Research and Analysis (CAMERA) is an eScience project to enable the microbial ecology community in managing the challenges of metagenomics analysis. CAMERA supports extensive metadata based data acquisition and access, as well as execution of metagenomics experiments through standard and customized scientific workflows. Users can use a wide range of community analysis tools to select and invoke integrated annotation of genomic datasets. Users can also search and sort information based on selected metadata over the underlying semantic database. We present the semantic data model of CAMERA and its integration with scientific workflow execution information. We also describe how this model is used to interlink related workflows, where outputs of previous workflow executions can be used as inputs by subsequent workflow executions. We demonstrate the effectiveness of our model and approach through scenarios built on currently supported CAMERA workflows and analysis. View full abstract»

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  • Blast Atlas: A Virtual Observatory for Genomes

    Publication Year: 2010 , Page(s): 57 - 64
    Save to Project icon | Request Permissions | Click to expandQuick Abstract | PDF file iconPDF (818 KB) |  | HTML iconHTML  

    Following the completion of the draft Human Genome in 2001, genomic sequence data is becoming available at an accelerating rate, fueled by advances in sequencing and computational technology. Meanwhile, large collections of astronomical and geospatial data have allowed the creation of virtual observatories, accessible throughout the world and requiring only commodity hardware. Through a combination of advances in data management, data mining and visualization, this infrastructure enables the development of new scientific and educational applications as diverse as galaxy classification and real-time tracking of earthquakes and volcanic plumes. In the present paper, we describe steps taken along a similar path towards a virtual observatory for genomes - an immersive three-dimensional visual navigation and query system for comparative genomic data. View full abstract»

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  • A Patch Model for Pandemic Influenza Simulation in Korea

    Publication Year: 2010 , Page(s): 65 - 71
    Save to Project icon | Request Permissions | Click to expandQuick Abstract | PDF file iconPDF (633 KB) |  | HTML iconHTML  

    For years, we have researched epidemiology model suitable for Korea based on InfluSim model, to analyze the spread of pandemic influenza. However, there is a problem with InfluSim, because the demographic characteristics and the movement of population within the nation are not considered in the research. For this reason, it is improper to draw preparedness against widespread of pandemic influenza from simulation results based on InfluSim. To overcome this problem, we have designed a patch model considering the nation as 16 separate regions. The patch model takes the 16 separate region's interaction with each other into account. It consists of InfluSim and network model. The network model takes the demographic characteristics and the population flow into account. This paper explains the patch model and also the simulation system based on the model. In addition, we show the result of the simulation based on the patch model. View full abstract»

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  • A Data Management Framework for Distributed Biomedical Research Environments

    Publication Year: 2010 , Page(s): 72 - 79
    Cited by:  Papers (2)
    Save to Project icon | Request Permissions | Click to expandQuick Abstract | PDF file iconPDF (611 KB) |  | HTML iconHTML  

    Biomedical research increasingly depends on access to and analysis of distributed medical and biomedical data. In biomedical research, datasets are often collected at multiple locations, as it is difficult to recruit required patient populations at one location. The sensitive nature of these datasets leads to a need for secure sharing methods that can work with distributed databases and image archives. The efficient implementation of such methods is complicated by the fact that the researchers who need to access data are often behind firewalls that prohibit inbound connections. This restriction, combined with large data volumes and many small files, leads to significant data transfer challenges. We present a data management framework suitable for such distributed biomedical research environments and describe its application in the context of FBIRN, a distributed data-sharing system for medical researchers. The framework includes security tools, catalogs for managing datasets, and a secure data transfer service. View full abstract»

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  • Evaluation of Visualization Approaches in a Biomedical Grid Environment

    Publication Year: 2010 , Page(s): 80 - 85
    Save to Project icon | Request Permissions | Click to expandQuick Abstract | PDF file iconPDF (557 KB) |  | HTML iconHTML  

    Advanced visualization technologies are gaining major importance to interpret, present and manipulate high dimensional biomedical data. Since new health technologies are constantly increasing in complexity, adequate information processing is required for diagnostics, therapy planning and treatment. The combination of advanced visualization resources and biomedical grid infrastructures is a promising approach to build dynamic and scalable problem solving environments for such tasks. Visualization then becomes the main issue in system-user interaction, and is therefore a crucial factor in the usefulness of the complete system for the domain researchers. In this paper, two remote visualization approaches to utilize the capabilities of such an environment are presented and evaluated. Evaluation criteria are performance, usability, adaptivity and functionality. Both, an open source and a commercial solution are considered. While the proprietary software shows better performance, the open source solution offers the advantage for seamless grid integration. View full abstract»

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