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e-Science, 2009. e-Science '09. Fifth IEEE International Conference on

Date 9-11 Dec. 2009

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Displaying Results 1 - 25 of 61
  • [Front cover]

    Page(s): C1
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  • [Title page i]

    Page(s): i
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  • [Title page iii]

    Page(s): iii
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  • [Copyright notice]

    Page(s): iv
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  • Table of contents

    Page(s): v - ix
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  • Preface

    Page(s): x - xi
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  • Organizing Committee

    Page(s): xii
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  • list-reviewer

    Page(s): xiii - xiv
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  • Alfalab: Construction and Deconstruction of a Digital Humanities Experiment

    Page(s): 1 - 5
    Save to Project icon | Request Permissions | Click to expandQuick Abstract | PDF file iconPDF (219 KB) |  | HTML iconHTML  

    This paper presents project 'Alfalab'. Alfalab is a collaborative frame work project of the Royal Netherlands Academy of Arts and Sciences (KNAW). It explores the success and fail factors for virtual research collaboration and supporting digital infrastructure in the Humanities. It does so by delivering a virtual research environment engineered through a virtual R&D collaborative and by drawing in use cases and feedback from Humanities researchers from two research fields: textual historical text research and historical GIS-application. The motivation for the project is found in a number of commonly stated factors that seem to be inhibiting general application of virtualized research infrastructure in the Humanities. The paper outlines the project's motivation, key characteristics and implementation. One of the pilot applications is described in greater detail. View full abstract»

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  • Topic Maps in the eHumanities

    Page(s): 6 - 13
    Save to Project icon | Request Permissions | Click to expandQuick Abstract | PDF file iconPDF (1495 KB) |  | HTML iconHTML  

    Topic maps is a semantic technology for the integration of heterogeneous data and the convenient deployment of domain specific and semantically enriched Web portals. Topic maps is already widely in productive usage in industry and administration. We demonstrate with six projects the current usage and the opportunities of topic maps in the eHumanities. The projects are CeDECA from University of Pavia, RAMLine from the London Royal Academy of Music, Pansori retrieval system from the Sungkyunkwan University Seoul, Musica migrans from the University of Leipzig, Collection of the Finnish National Gallery, and text and semantic from Signum in Pisa. View full abstract»

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  • An Image Processing Portal and Web-Service for the Study of Ancient Documents

    Page(s): 14 - 19
    Save to Project icon | Request Permissions | Click to expandQuick Abstract | PDF file iconPDF (915 KB) |  | HTML iconHTML  

    Linking up two projects that are dedicated to facilitate the work of documentary scholars, this paper presents image processing algorithms tailored to the study of ancient documents and how they have been made available to the users through a portal that calls upon a web-service exploiting grid computational power. To that end, image processing algorithms were wrapped to fit into the National Grid Service (NGS) Uniform Execution Environment; the data model of an existing Virtual Research Environment (VRE-SDM) was extended; JSR-168 compliant portlets were developed to facilitate secure and seamless distributed image analysis; and a GridSAM interface between the portal and the NGS-installed algorithms was developed. The outcomes of the project include: a web-based application, a proof of concept for the usability of the VRE-SDM platform, an opportunity for wider dissemination for the image processing algorithms, and a proof of feasibility for the use of the NGS for Humanities applications. View full abstract»

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  • CLAROS - Bringing Classical Art to a Global Public

    Page(s): 20 - 27
    Save to Project icon | Request Permissions | Click to expandQuick Abstract | PDF file iconPDF (667 KB) |  | HTML iconHTML  

    CLAROS (Classical Art Research Online Services; www.clarosweb.org) is an international interdisciplinary research initiative led by the University of Oxford (Humanities and Mathematics and Physical Sciences), hosted by the Oxford e-Research Centre (OeRC, www.oerc.ox.ac.uk), and inspired by the Beazley Archive (www.beazley.ox.ac.uk) participating in EU R&D projects. During 2009, a pump-priming grant from the University's Fell Fund enabled CLAROS to integrate on line more than two million records and images held in research centres in Oxford, Paris, Cologne and Berlin. CLAROS uses CIDOC CRM (http://cidoc.ics.forth.gr/), developed under UNESCO's ICOM (http://icom.museum/), to map across datasets and a portfolio of Open Source software to deliver them swiftly to a broad range of global users. Data web applications for integration are being developed by Zoology (http://ibrg.zoo.ox.ac.uk/), image recognition by Engineering Science (www.robots.ox.ac.uk/~vgg/), and artificial intelligence by the Oxford Internet Institute (www.oii.ox.ac.uk). CLAROS will welcome new institutional members and engage with the public to document art and disseminate results. View full abstract»

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  • Integrating Full-Text Search and Linguistic Analyses on Disperse Data for Humanities and Social Sciences Research Projects

    Page(s): 28 - 32
    Save to Project icon | Request Permissions | Click to expandQuick Abstract | PDF file iconPDF (240 KB) |  | HTML iconHTML  

    The research reported in this paper is part of the activities carried out within the CLARIN (common language resources and technology infrastructure) project, a large-scale pan-European project to create, coordinate and make language resources and technologies (LRT) available and readily useable. CLARIN is devoted to the creation of a persistent and stable infrastructure serving the needs of the European humanities and social sciences (HSS) research community. HSS researchers will be able to efficiently access distributed resources and apply analysis and exploitation tools relevant for their research. Hereby we present a real use case addressed as a CLARIN scenario and the implementation of a demonstrator that enables us to foresee the potential problems and contributes to the planning of the implementation phase. It deals with how to support researchers interested in harvesting and analyzing data from historical press archives. Therefore, we address the integration and interoperability of distributed and heterogeneous research data and analysis tools. View full abstract»

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  • Building Bridges between Islands of Data - An Investigation into Distributed Data Management in the Humanities

    Page(s): 33 - 39
    Save to Project icon | Request Permissions | Click to expandQuick Abstract | PDF file iconPDF (280 KB) |  | HTML iconHTML  

    Ancient documents represent a primary source for research in the humanities. A substantial body of digital material has evolved containing information about these documents. Unfortunately these digital resources are often held within myriad locations, owned by a range of groups or individuals, are held within a diverse range of formats and are either unavailable or are available only in isolation. This paper describes a successful investigation into using the OGSA-DAI distributed data management software to build bridges between these islands of data and so to facilitate navigation across a larger data space than is otherwise achievable. An overview of a proof-of-concept that was developed is given along with the technical challenges encountered. Discussion from researchers in the humanities about such an architecture reveals the possibility of creating virtual data centres for the coordinated sharing of such resources. It also raises important questions as to how distributed data resources can be meaningfully federated and queried. View full abstract»

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  • An Ontology Based Framework for the Preservation of Interactive Multimedia Performances

    Page(s): 40 - 44
    Save to Project icon | Request Permissions | Click to expandQuick Abstract | PDF file iconPDF (448 KB) |  | HTML iconHTML  

    Interactive multimedia and human-computer interaction technologies are effecting and contributing towards a wide range of developments in many different subject areas including contemporary performing arts. These technologies have facilitated the developments and advancements of augmented and virtual instruments for interactive music performance, interactive installation, many aspects of technology-enhanced learning (TEL) and others. These systems typically involve several different digital objects including software as well as data that are necessary for the performance and/or data captured/generated during the performance that may be invaluable to understand the performance. Consequently, the preservation of interactive multimedia systems and performances is an important step to ensure possible future re-performances as well as preserving the artistic style and heritage of the art form. This paper presents the CASPAR framework (developed within the CASPAR EC IST project) for the preservation of interactive multimedia performances (IMP) and introduces an IMP archival system that has been developed based on the CASPAR framework and components. This paper also discusses the main functionalities and validation of the IMP archival system developed. View full abstract»

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  • The SweDat Project and Swedia Database for Phonetic and Acoustic Research

    Page(s): 45 - 49
    Save to Project icon | Request Permissions | Click to expandQuick Abstract | PDF file iconPDF (386 KB) |  | HTML iconHTML  

    The project described here may be seen as a continuation of an earlier project, SweDia 2000, aimed at transforming the database collected in that project to a full-fledged e-science database. The database consists of recordings of Swedish dialects from 107 locations in Sweden and Swedish speaking parts of Finland. The goal of the present project is to make the material searchable in a flexible and simple way to make it available to a much wider sector of the research community than is the case at present. The database will be accessible over the Internet via user-friendly interfaces specifically designed for this type of data. Other more specialized research interfaces will also be designed to facilitate phonetic acoustic research and orientation of the database. View full abstract»

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  • Supporting the Running and Analysis of Trials of Web-Based Behavioural Interventions: The LifeGuide

    Page(s): 50 - 57
    Save to Project icon | Request Permissions | Click to expandQuick Abstract | PDF file iconPDF (1408 KB) |  | HTML iconHTML  

    Behavioural interventions packages of advice and support for behaviour change are one of the most important methodologies and technologies employed by social scientists for understanding and changing behaviour. A typical web-based behavioural intervention study includes the designing, deploying, piloting and trialling of the intervention as well as data analysis. We have developed a research environment named LifeGuide, which covers the full scope of this process, enabling social scientists to carry out intervention studies with minimal technical expertise. In this paper, we present how the LifeGuide can assist and accelerate intervention research, particularly focusing on supporting the running and analysis of trials of web-based behavioural interventions along with the case study of an intervention that has been developed within the LifeGuide. View full abstract»

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  • Phylogenetic Predictions on Grids

    Page(s): 58 - 65
    Save to Project icon | Request Permissions | Click to expandQuick Abstract | PDF file iconPDF (736 KB) |  | HTML iconHTML  

    A phylogenetic or evolutionary tree is constructed from a set of species or DNA sequences and depicts the relatedness between the sequences. Predictions of future sequences in a phylogenetic tree are important for a variety of applications including drug discovery, pharmaceutical research and disease control. In this work, we predict future DNA sequences in a phylogenetic tree using cellular automata. Cellular automata are used for modeling neighbor-dependent mutations from an ancestor to a progeny in a branch of the phylogenetic tree. Since the number of possible ways of transformations from an ancestor to a progeny is huge, we use computational grids and middleware techniques to explore the large number of cellular automata rules used for the mutations. We use the popular and recurring neighbor-based transitions or mutations to predict the progeny sequences in the phylogenetic tree. We performed predictions for three types of sequences, namely, triose phosphate isomerase, pyruvate kinase, and polyketide synthase sequences, by obtaining cellular automata rules on a grid consisting of 29 machines in 4 clusters located in 4 countries, and compared the predictions of the sequences using our method with predictions by random methods. We found that in all cases, our method gave about 40% better predictions than the random methods. View full abstract»

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  • Increasing the Efficiency of Data Storage and Analysis Using Indexed Compression

    Page(s): 66 - 71
    Save to Project icon | Request Permissions | Click to expandQuick Abstract | PDF file iconPDF (363 KB) |  | HTML iconHTML  

    The massive data sets produced by the high- throughput, multidimensional mass spectrometry instruments used in proteomics create challenges in data acquisition, storage and analysis. Data compression can help mitigate some of these problems but at the cost of less efficient data access, which directly impacts the computational time of data analysis. We have developed a compression methodology that 1) is optimized for a targeted mass spectrometry proteomics data set and 2) provides the benefits of size and speed from compression while increasing analysis efficiency by allowing extraction of segments of uncompressed data from a file without having to uncompress the entire file. This paper describes our compression algorithm, presents comparative metrics of compression size and speed, and explores approaches for applying the algorithm to a generalized data set. View full abstract»

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  • User-Level Virtual Network Support for Sky Computing

    Page(s): 72 - 79
    Save to Project icon | Request Permissions | Click to expandQuick Abstract | PDF file iconPDF (899 KB) |  | HTML iconHTML  

    With the emergence of multiple cloud providers of Infrastructure-as-a-Service, it becomes possible to envision a near-future when high-performance computing users could combine services from different clouds to access huge numbers of resources. However, as more administrative privileges are exposed to end users, providers are required to deploy network security measures that present challenges to the network virtualization technologies that are needed to enable inter-cloud communication. This paper studies these challenges and proposes techniques to enable unmodified applications on resources across distinct clouds. The techniques are implemented in TinyViNe, an extension to ViNe, a virtual networking technology for distributed resources in different administrative domains. The results of evaluating TinyViNe on a WAN-based testbed across three sites are reported for a bioinformatics application (BLAST) and MPI benchmarks. The results confirm that TinyViNe enables cross-cloud computing while having little impact on application performance. TinyViNe also has auto-configuration and ¿download-and-run¿ capabilities for easy deployment by users who are not knowledgeable about networking. View full abstract»

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  • Strategies for Network Motifs Discovery

    Page(s): 80 - 87
    Save to Project icon | Request Permissions | Click to expandQuick Abstract | PDF file iconPDF (266 KB) |  | HTML iconHTML  

    Complex networks from domains like Biology or Sociology are present in many e-Science data sets. Dealing with networks can often form a workflow bottleneck as several related algorithms are computationally hard. One example is detecting characteristic patterns or "network motifs" - a problem involving subgraph mining and graph isomorphism. This paper provides a review and runtime comparison of current motif detection algorithms in the field. We present the strategies and the corresponding algorithms in pseudo-code yielding a framework for comparison. We categorize the algorithms outlining the main differences and advantages of each strategy. We finally implement all strategies in a common platform to allow a fair and objective efficiency comparison using a set of benchmark networks. We hope to inform the choice of strategy and critically discuss future improvements in motif detection. View full abstract»

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  • An Architecture for Real Time Data Acquisition and Online Signal Processing for High Throughput Tandem Mass Spectrometry

    Page(s): 88 - 93
    Save to Project icon | Request Permissions | Click to expandQuick Abstract | PDF file iconPDF (416 KB) |  | HTML iconHTML  

    Independent, greedy collection of data events using simple heuristics results in massive over-sampling of the prominent data features in large-scale studies over what should be achievable through ¿intelligent", online acquisition of such data. As a result, data generated are more aptly described as a collection of a large number of small experiments rather than a true large-scale experiment. Nevertheless, achieving ¿intelligent¿, online control requires tight interplay between state-of-the-art, data-intensive computing infrastructure developments and analytical algorithms. In this paper, we propose a Software Architecture for Mass spectrometry-based Proteomics coupled with Liquid chromatography Experiments (SAMPLE) to develop an ¿intelligent¿ online control and analysis system to significantly enhance the information content from each sensor (in this case, a mass spectrometer). Using online analysis of data events as they are collected and decision theory to optimize the collection of events during an experiment, we aim to maximize the information content generated during an experiment by the use of pre-existing knowledge to optimize the dynamic collection of events. View full abstract»

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  • Sharing and Reusing Cancer Image Segmentation Algorithms Using Scientific Workflows: Pros and Cons

    Page(s): 94 - 101
    Save to Project icon | Request Permissions | Click to expandQuick Abstract | PDF file iconPDF (529 KB) |  | HTML iconHTML  

    Image analysis researchers would benefit considerably by sharing and reusing image processing algorithms. We consider some of the issues that researchers face in trying to provide algorithms in a shareable and reusable form illustrating our approach in the context of medical imaging needs and workflow for colorectal cancer. We consider the use of workflow as a model for developing and reusing components of medical imaging and specifically we consider a solution built using .Net and Windows Workflow Foundation. View full abstract»

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  • A Cloud-Based Interactive Application Service

    Page(s): 102 - 109
    Save to Project icon | Request Permissions | Click to expandQuick Abstract | PDF file iconPDF (749 KB) |  | HTML iconHTML  

    Accessing, running and sharing applications and data presents researchers with many challenges. Cloud computing and social networking technologies have the potential to simplify or eliminate many of these challenges. Cloud computing technologies can provide scientists with transparent and on-demand access to applications served over the Internet in a dynamic and scalable manner. Social networking technologies provide a means for easily sharing applications and data. In this paper we present an on-line/on-demand interactive application service. The service is built on a cloud computing infrastructure that dynamically provisions virtualized application servers based on user demand. An open source social networking platform is leveraged to establish a portal front end that enables applications and results to be easily shared between researchers. Furthermore, the service works with existing/legacy applications without requiring any modifications. View full abstract»

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  • eScience for Sea Science: A Semantic Scientific Knowledge Infrastructure for Marine Scientists

    Page(s): 110 - 117
    Save to Project icon | Request Permissions | Click to expandQuick Abstract | PDF file iconPDF (1187 KB) |  | HTML iconHTML  

    The COastal and Marine Perception Application for Scientific Scholarship (COMPASS) is a knowledge infrastructure that supports enhanced discovery of scientific resources, including publications, data sets and web services. It provides users with the ability to discover resources on the basis of domain knowledge using ontologies, and scientific knowledge, including the scientific models, theories and methods that were used to conduct the research described by the resource. The application includes an architecture that adopts standards from the geospatial information community to ensure interoperability between repositories and allow interaction with content from digital libraries. The architecture shows how ontologies can be used as a registry for an interoperable infrastructure. A prototype was successfully implemented and evaluated with users, finding enthusiasm and support for the approach, with some suggestions for improvements of the prototype implementation. View full abstract»

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