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2009 Fifth IEEE International Conference on e-Science最新文献

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Topic Maps in the eHumanities 电子人文学科的主题图
Pub Date : 2009-12-09 DOI: 10.1109/e-Science.2009.9
Lutz Maicher, Khalil Ahmed, Alida Isolani, A. Kivelä, S. Oh, A. Pitts, Salvatore Vassallo
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.
主题图是一种语义技术,用于集成异构数据和方便部署特定领域和语义丰富的web门户。主题图已经在工业和行政管理中得到了广泛的应用。我们用六个项目来展示主题图在电子人文学科中的当前使用和机会。这些项目包括来自帕维亚大学的CeDECA、来自伦敦皇家音乐学院的RAMLine、来自首尔成均馆大学的盘索里检索系统、来自莱比锡大学的Musica migrans、芬兰国家美术馆的Collection of Finnish National Gallery以及来自比萨Signum的Text and Semantic。
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引用次数: 1
The Role of OAIS Representation Information in the Digital Curation of Crystallography Data OAIS表示信息在晶体学数据数字化管理中的作用
Pub Date : 2009-12-09 DOI: 10.1109/E-SCIENCE.2009.27
M. Patel, S. Coles, D. Giaretta, S. Rankin, B. McIlwrath
Reusable high quality data are emerging as the raw material of contemporary e-science. Large volumes of scientific data are now “born-digital” and need to be curated to facilitate use and reuse. Representation Information (RI) as defined by the OAIS Reference Model is increasingly recognised as being vital to the long term curation and preservation of meaningful and reliable digital data. This paper is concerned with an investigation of RI for crystallography data and its role in the curation, maintenance and management of such data. We describe how the explicit recording of relevant RI can facilitate long term access and maintain intelligibility of the Crystallographic Information File format (a critical file format in the crystallography domain).
可重复使用的高质量数据正在成为当代电子科学的原材料。现在,大量的科学数据是“天生的数字”,需要加以整理,以促进使用和再利用。由OAIS参考模型定义的表示信息(RI)越来越被认为是长期管理和保存有意义和可靠的数字数据的关键。本文研究了晶体学数据的RI及其在这些数据的管理、维护和管理中的作用。我们描述了相关RI的明确记录如何促进长期访问并保持晶体信息文件格式(晶体学领域的关键文件格式)的可理解性。
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引用次数: 5
CLAROS - Bringing Classical Art to a Global Public CLAROS -将古典艺术带给全球公众
Pub Date : 2009-12-09 DOI: 10.1109/e-Science.2009.11
D. Kurtz, G. Parker, D. Shotton, G. Klyne, Florian Schroff, Andrew Zisserman, Y. Wilks
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.
CLAROS(古典艺术研究在线服务;www.clarosweb.org)是由牛津大学(人文科学、数学和物理科学)牵头、牛津电子研究中心(OeRC, www.oerc.ox.ac.uk)主持、参与欧盟研发项目的比兹利档案馆(www.beazley.ox.ac.uk)启发的国际跨学科研究计划。2009年,大学费尔基金的资助使CLAROS得以将牛津、巴黎、科隆和柏林的研究中心保存的200多万份记录和图像整合到网上。CLAROS使用联合国教科文组织ICOM (http://icom.museum/)开发的CIDOC CRM (http://cidoc.ics.forth.gr/)来绘制跨数据集和开源软件组合的地图,以便将它们迅速提供给广泛的全球用户。动物学(http://ibrg.zoo.ox.ac.uk/)、工程科学(www.robots.ox.ac.uk/~vgg/)、牛津因特网研究所(www.oii.ox.ac.uk)分别开发了整合数据的网络应用程序。CLAROS将欢迎新的机构成员,并与公众一起记录艺术和传播结果。
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引用次数: 26
Expressive Reusable Workflow Templates 富有表现力的可重用工作流模板
Pub Date : 2009-12-09 DOI: 10.1109/E-SCIENCE.2009.55
Y. Gil, Paul T. Groth, V. Ratnakar, Christian Fritz
Workflow systems can manage complex scientific applications with distributed data processing. Although some workflow systems can represent collections of data with very compact abstractions and manage their execution efficiently, there are no approaches to date to manage collections of application components required to express some scientific applications. We present an approach to handle collections of components and data alike in expressive workflow templates whose basic structure is reusable. We also present an algorithm that can elaborate abstract compact workflow templates into execution-ready workflows that enumerate all computations to be carried out. We implemented the proposed approach in the Wings workflow system. Our work is motivated by real-world complex scientific applications that require handling of nested collections of both components and data.
工作流系统可以通过分布式数据处理来管理复杂的科学应用。尽管一些工作流系统可以用非常紧凑的抽象来表示数据集合,并有效地管理它们的执行,但迄今为止还没有方法来管理表达某些科学应用程序所需的应用程序组件集合。提出了一种在基本结构可重用的表达性工作流模板中处理组件和数据集合的方法。我们还提出了一种算法,可以将抽象的紧凑工作流模板精心设计成可执行的工作流,枚举所有要执行的计算。我们在Wings工作流系统中实现了该方法。我们的工作是由现实世界中复杂的科学应用程序驱动的,这些应用程序需要处理组件和数据的嵌套集合。
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引用次数: 38
Towards Lensfield - Data Management, Processing and Semantic Publication for Vernacular e-Science 面向Lensfield——面向白话电子科学的数据管理、处理与语义出版
Pub Date : 2009-12-09 DOI: 10.1109/e-Science.2009.56
N. Day, J. Downing, L. Hawizy, Nico Adams, Peter Murray-Rust
Lensfield is a desktop and filesystem-based tool designed as a “personal data management assistant” for the scientist. It combines distributed version control (DVCS), software transaction memory (STM) and linked open data (LOD) publishing to create a novel data management, processing and publication tool. The application “just looks after” these technologies for the scientist, providing simple interfaces for typical uses. It is built with Clojure and includes macros which define steps in a common workflow. Functions and Java libraries provide facilities for automatic processing of data which is ultimately published as RDF in a web application. The progress of data processing is tracked by a fine-grained data structure that can be serialized to disk, with the potential to include manual steps and programmatic interrupts in largely automated processes through seamless resumption. Flexibility in operation and minimizing barriers to adoption are major design features.
Lensfield是一款基于桌面和文件系统的工具,是为科学家设计的“个人数据管理助理”。它结合了分布式版本控制(DVCS)、软件事务存储器(STM)和链接开放数据(LOD)发布,创建了一种新颖的数据管理、处理和发布工具。该应用程序为科学家“照看”这些技术,为典型用途提供简单的接口。它是用Clojure构建的,包含了定义通用工作流步骤的宏。函数和Java库为数据的自动处理提供了便利,这些数据最终作为RDF在web应用程序中发布。数据处理的过程由细粒度的数据结构跟踪,该数据结构可以序列化到磁盘上,并且可以通过无缝恢复在很大程度上自动化的过程中包含手动步骤和编程中断。操作的灵活性和最大限度地减少采用障碍是主要的设计特点。
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引用次数: 1
DryadLINQ for Scientific Analyses 用于科学分析的干燥linq
Pub Date : 2009-12-09 DOI: 10.1109/e-Science.2009.53
Jaliya Ekanayake, Thilina Gunarathne, G. Fox, A. S. Balkir, Christophe Poulain, N. Araujo, R. Barga
Applying high level parallel runtimes to data/compute intensive applications is becoming increasingly common. The simplicity of the MapReduce programming model and the availability of open source MapReduce runtimes such as Hadoop, are attracting more users to the MapReduce programming model. Recently, Microsoft has released DryadLINQ for academic use, allowing users to experience a new programming model and a runtime that is capable of performing large scale data/compute intensive analyses. In this paper, we present our experience in applying DryadLINQ for a series of scientific data analysis applications, identify their mapping to the DryadLINQ programming model, and compare their performances with Hadoop implementations of the same applications.
将高级并行运行时应用于数据/计算密集型应用程序正变得越来越普遍。MapReduce编程模型的简单性和开源MapReduce运行时(如Hadoop)的可用性正在吸引更多的用户使用MapReduce编程模型。最近,微软发布了学术用途的DryadLINQ,允许用户体验一种新的编程模型和能够执行大规模数据/计算密集型分析的运行时。在本文中,我们介绍了我们在一系列科学数据分析应用中应用DryadLINQ的经验,确定了它们到DryadLINQ编程模型的映射,并将它们的性能与相同应用的Hadoop实现进行了比较。
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引用次数: 44
A New Fault Tolerance Heuristic for Scientific Workflows in Highly Distributed Environments Based on Resubmission Impact 基于重提交影响的高分布环境下科学工作流容错启发式算法
Pub Date : 2009-12-09 DOI: 10.1109/e-Science.2009.51
Kassian Plankensteiner, R. Prodan, T. Fahringer
Even though highly distributed environments such as Clouds and Grids are increasingly used for e-Science high performance applications, they still cannot deliver the robustness and reliability needed for widespread acceptance as ubiquitous scientific tools. To overcome this problem, existing systems resort to fault tolerance mechanisms such as task replication and task resubmission. In this paper we propose a new heuristic called Resubmission Impact to enhance the fault tolerance support for scientific workflows in highly distributed systems. In contrast to related approaches, our method can be used effectively on systems even in the absence of historic failure trace data. Simulated experiments of three real scientific workflows in the Austrian Grid environment show that our algorithm drastically reduces the resource waste compared to conservative task replication and resubmission techniques, while having a comparable execution performance and only a slight decrease in the success probability.
尽管高度分布式的环境(如云和网格)越来越多地用于e-Science高性能应用程序,但它们仍然无法提供广泛接受作为无处不在的科学工具所需的健壮性和可靠性。为了克服这个问题,现有系统采用容错机制,如任务复制和任务重新提交。本文提出了一种新的启发式方法——重提交影响,以增强对高度分布式系统中科学工作流的容错支持。与相关方法相比,即使在没有历史故障跟踪数据的情况下,我们的方法也可以有效地用于系统。在奥地利网格环境下对三个真实科学工作流的模拟实验表明,与保守的任务复制和重新提交技术相比,我们的算法大大减少了资源浪费,同时具有相当的执行性能,成功概率仅略有下降。
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引用次数: 48
Virtual Microscopy and Analysis Using Scientific Workflows 使用科学工作流程的虚拟显微镜和分析
Pub Date : 2009-12-09 DOI: 10.1109/e-Science.2009.41
D. Abramson, B. Bethwaite, M. N. Dinh, C. Enticott, Stephen Firth, S. Garic, I. Harper, M. Lackmann, H. Nguyen, Tirath Ramdas, A. Russel, Stefan Schek, Mary Vail
Most commercial microscopes are stand-alone instruments, controlled by dedicated computer systems. These provide limited storage and processing capabilities. Virtual microscopes, on the other hand, link the image capturing hardware and data analysis software into a wide area network of high performance computers, large storage devices and software systems. In this paper we discuss extensions to Grid workflow engines that allow them to execute scientific experiments on virtual microscopes. We demonstrate the utility of such a system in a biomedical case study concerning the imaging of cancer and antibody based therapeutics.
大多数商用显微镜都是由专用计算机系统控制的独立仪器。它们提供有限的存储和处理能力。另一方面,虚拟显微镜将图像捕获硬件和数据分析软件连接到一个由高性能计算机、大型存储设备和软件系统组成的广域网中。在本文中,我们讨论了网格工作流引擎的扩展,使他们能够在虚拟显微镜上执行科学实验。我们在一个生物医学案例研究中展示了这种系统的效用,该研究涉及癌症成像和基于抗体的治疗。
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引用次数: 6
eScience for Sea Science: A Semantic Scientific Knowledge Infrastructure for Marine Scientists 面向海洋科学的eScience:面向海洋科学家的语义科学知识基础结构
Pub Date : 2009-12-09 DOI: 10.1109/e-Science.2009.24
Kristin Stock, Anne Robertson, F. Reitsma, T. Stojanovic, M. Bishr, D. Medyckyj-Scott, J. Ortmann
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.
海岸和海洋感知科学奖学金应用(COMPASS)是一个知识基础设施,支持加强科学资源的发现,包括出版物、数据集和网络服务。它为用户提供了在使用本体的领域知识和科学知识的基础上发现资源的能力,包括用于进行资源所描述的研究的科学模型、理论和方法。该应用程序包括采用地理空间信息社区标准的体系结构,以确保存储库之间的互操作性,并允许与数字图书馆的内容进行交互。该体系结构展示了如何将本体用作可互操作基础结构的注册中心。成功地实现了一个原型,并与用户进行了评估,找到了对该方法的热情和支持,并提出了一些改进原型实现的建议。
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引用次数: 12
Problems and Approaches of Workflow Scheduling in MediGRID MediGRID中工作流调度的问题与方法
Pub Date : 2009-12-09 DOI: 10.1109/e-Science.2009.39
Dietmar Sommerfeld, H. Richter
We describe four problems inherent to Grid scheduling that could be identified by means of measurements in the D-Grid. These problems make meta-scheduling nearly always a delicate task. In the face of this, we developed a new hybrid methodology to schedule application workflows which presumably supersedes existing methods. Our algorithm combines existing scheduling strategies for the Grid and for workflows, and it additionally employs three prediction methods for the expected queue waiting times. Three site scenarios could be identified where one respective prediction works best. To meet the dynamic characteristics of heterogeneous Grid resources, we use a list scheduling heuristic to perform full-ahead planning of workflow tasks based on execution time predictions, and then distribute Grid jobs just-in-time according to resource performance predictions calculated from up-to-date monitoring data.
我们描述了网格调度固有的四个问题,这些问题可以通过D-Grid中的测量来识别。这些问题使得元调度几乎总是一项微妙的任务。面对这种情况,我们开发了一种新的混合方法来调度应用程序工作流,它可能会取代现有的方法。我们的算法结合了网格和工作流的现有调度策略,并采用了三种预测队列等待时间的方法。可以确定三个站点场景,其中一个各自的预测效果最好。为了满足异构网格资源的动态特性,我们采用列表调度启发式算法,基于执行时间预测对工作流任务进行全提前规划,然后根据最新监控数据计算出的资源性能预测及时分发网格作业。
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引用次数: 4
期刊
2009 Fifth IEEE International Conference on e-Science
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