检索结果-内蒙古大学图书馆

Annual IEEE Symposium on Computer-Based Medical Systems

作者： Sonja Holl Morris Riedel Bastian Demuth Mathilde Romberg Achim Streit Vinod Kasam Forschungszentrum Juelich Juelich Supercomputing Center Juelich Germany Schloss Birlinghoven Fraunhofer Institute for Algorithms and Scientific Computing Sankt Augustin Germany

In the last decade, life science applications have become more and more integrated into e-Science environments, hence they are typically very demanding, both in terms of computational capabilities and data capacities. Especially the access to life science applications, embedded in such environments via Grid clients still constitutes a major hurdle for scientists that do not have an IT background. Life science applications often comprise a whole set of small programs instead of a single executable. Many of the graphical Grid clients are not perfectly suited for these types of applications, as they often assume that Grid jobs will run a single executable instead of a set of chained executions (i.e. sequences). This means that in order to execute a sequence of multiple programs on a single Grid resource, piping data from one program to the next, the user would have to run a hand-written shell script. Otherwise each program is independently scheduled as a Grid job, which causes unnecessary file transfers between the jobs, even if they are scheduled on the same resource. We present a generic solution to this problem and provide a reference implementation, which seamlessly integrates with the Grid middleware UNICORE. Our approach focuses on a comfortable user interface for the creation of such program sequences, validated in UNICORE-driven HPC-based Grids. Thus, we applied our approach in order to provide support for the usage of the AMBER package (a widely-used collection of programs for molecular dynamics simulations) within Grid workflows. We finally provide a scientific use case of our approach leveraging the interoperability of two different scientific infrastructures that represents an instance of the infrastructure interoperability reference model.

关键词： Middleware Biology computing Sequences Biological system modeling Bioinformatics scientific computing User interfaces Packaging Collaborative work Chemistry

来源：评论

学校读者我要写书评

暂无评论

Grid Middleware and Services 2008

引用

2008年

作者： Domenico Talia Ramin Yahyapour Wolfgang Ziegler

ISBN: (数字)9780387784465

ISBN: (纸本)9780387784458

Grid Middleware and Services: Challenges and Solutions is the eighth volume of the CoreGRID series. The CoreGrid Proceedings is the premiere European event on Grid computing. This book aims to strengthen and advance scientific and technological excellence in the area of Grid computing. The main focus in this volume is on Grid middleware and service level agreement. Grid middleware and Grid services are two pillars of grid computing systems and applications. This book includes high-level contributions by leading researchers in both areas and presents current solutions together with future challenges. This volume includes sections on knowledge and data management on grids, Grid resource management and scheduling, Grid information, resource and workflow monitoring services, and service level agreements. Grid Middleware and Services: Challenges and Solutions is designed for a professional audience, composed of researchers and practitioners in industry. This volume is also suitable for graduate-level students in computer science.

关键词：

来源：评论

学校读者我要写书评

暂无评论

Grid-enabled virtual screening against malaria

Grid-enabled virtual screening against malaria

引用

作者： Jacq, N. Salzemann, J. Jacq, F. Legré, Y. Medernach, E. Montagnat, J. Maaß, A. Breton, V. Schwichtenberg, H. Sridhar, M. Kasam, V. Zimmermann, M. Hofmann, M. Breton, V. Laboratoire de Physique Corpusculaire Université Blaise Pascal IN2P3-CNRS UMR 6533 24 Avenue des Landais 63177 Aubière France Communication and Systèmes Grenoble France Informatique Signaux et Systèmes Université de Nice Sophia Antipolis CNRS UMR 6070 Sophia Antipolis France Department of Simulation Engineering Fraunhofer Institute for Algorithms and Scientific Computing Sankt Augustin Germany Department of Bioinformatics Fraunhofer Institute for Algorithms and Scientific Computing Sankt Augustin Germany

WISDOM is an international initiative to enable a virtual screening pipeline on a Grid infrastructure. Its first attempt was to deploy large scale in silico docking on a public Grid infrastructure. Protein-ligand docking is about computing the binding energy of a protein target to a library of potential drugs using a scoring algorithm. Previous deployments were either limited to one cluster, to Grids of clusters in the tightly protected environment of a pharmaceutical laboratory or to desktop Grids. The first large scale docking experiment ran on the EGEE Grid production service from 11 July 2005 to 19 August 2005 against targets relevant to research on malaria and saw over 41 million compounds docked for the equivalent of 80 years of CPU time. Up to 1,700 computers were simultaneously used in 15 countries around the world. Issues related to the deployment and the monitoring of the in silico docking experiment as well as experience with Grid operation and services are reported in the paper. The main problem encountered for such a large scale deployment was the Grid infrastructure stability. Although the overall success rate was above 80%, a lot of monitoring and supervision was still required at the application level to resubmit the jobs that failed. But the experiment demonstrated how Grid infrastructures have a tremendous capacity to mobilize very large CPU resources for well targeted goals during a significant period of time. This success leads to a second computing challenge targeting avian flu neuraminidase N1. © Springer Science + Business Media B.V. 2007.

关键词： Grid computing

来源：评论

学校读者我要写书评

暂无评论

@neurIST - Towards a System Architecture for Advanced Disease Management through Integration of Heterogeneous Data, computing, and Complex Processing Services

@neurIST - Towards a System Architecture for Advanced Diseas...

引用

Annual IEEE Symposium on Computer-Based Medical Systems

作者： Hariharan Rajasekaran Luigi Lo Iacono Peer Hasselmeyer Jochen Fingberg Paul Summers Siegfried Benkner Gerhard Engelbrecht Antonio Arbona Alessandro Chiarini Christoph M. Friedrich Martin Hofmann-Apitius Kai Kumpf Bob Moore Philippe Bijlenga Jimison Iavindrasana Henning Mueller Rod D. Hose Robert Dunlop Alejandro Frangi IT Research Division NEC Laboratories Europe NEC Europe Limited Sankt Augustin Germany University of Oxford Oxford UK Institute of Scientific Computing University of Technology Vienna Vienna Austria Grid Systems S. A. Palma de Mallorca Spain B3C BioComputing Competence Centre Bologna Italy Fraunhofer Institute SCAI Sankt Augustin Germany IDAC Ireland Limited Ireland University Hospitals of Geneva Geneva Switzerland University of Sheffield Sheffield UK Infermed Limited UK Information & Communications Technology Department Universitat Pompeu Fabra Barcelona Spain

This paper presents the system architecture of the @neurIST project, which aims at supporting the research and treatment of cerebral aneurysms by bringing together heterogeneous data, computing and complex processing services. The architecture is generic enough to adapt it to the treatment of other diseases beyond cerebral aneurysms. The paper describes the generic requirements of the system and presents the architecture, applications and middleware technologies used to realise the system and highlights the innovations in @neurIST.

关键词： Computer architecture Diseases Aneurysm Costs Europe Project management Medical treatment Medical diagnostic imaging National electric code Hospitals

来源：评论

学校读者我要写书评

暂无评论

Reconstruction of chemical molecules from images

Reconstruction of chemical molecules from images

引用

29th Annual International Conference of IEEE-EMBS, Engineering in Medicine and Biology Society, EMBC'07

作者： Algorri, Maria-Elena Zimmermann, Marc Friedrich, Christoph M. Akle, Santiago Hofmann-Apitius, Martin Department of Digital Systems Instituto Tecnologico Autonomo de Mexico Mexico City Dept. of Bioinformatics Fraunhofer Institute for Algorithms and Scientific Computing Sankt Augustin Germany

ISBN: (纸本)1424407885

We have developed a system for the automatic reconstruction of chemical molecules from images. The system takes as input an electronically produced image of a chemical molecule and produces an SDF file containing the complete chemical description of the molecule. The SDF file can then be read and used by most chemical computer programs. Our system finds extensive application in information extraction problems where the molecule images contained in chemical documents need to be rendered computer readable. We have benchmarked our system against a commercially available product and have also tested it using chemical databases of several thousand images. The system can be parameterized to reconstruct images of different sources and different characteristics. © 2007 IEEE.

关键词： Image reconstruction

来源：评论

学校读者我要写书评

暂无评论

Simulated Reality in Automotive Design

Simulated Reality in Automotive Design

引用

International Conference on Cyberworlds

作者： Andre Stork Clemens-August Thole Stanislav Klimenko Igor Nikitin Lialia Nikitina Yuri Astakhov IGD Fraunhofer Institute of Computer Graphics Research (IGD) Darmstadt Germany SCAI Fraunhofer Institute for Algorithms and Scientific Computing Darmstadt Germany ICPT Institute of Computing for Physics and Technology Moscow Russia Mathematical Institute University of Cologne Germany

In this paper we introduce Simulated Reality (SR) as a new concept for the interplay between simulation, optimization and interactive visualization. We see SR as a new metaphor for the interactive visual exploration of simulation and optimization results. The vision of Simulated Reality implies interactive behavior of simulations. Fact is today that simulations might still need hours of computation time, especially in crash worthiness. This paper shows approaches to come closer to the vision of SR. Combining design of experiments methods, metamodeling, new interpolation schemes and innovative graphics methods, we enable to user to interact with simulation parameters, optimization criteria and come to a new interpolated crash result within seconds. The approaches have been successfully applied for solution of real life car design optimization problems.

关键词： Automotive engineering Computational modeling Strontium Design optimization Visualization Computer crashes Design methodology Metamodeling Interpolation Graphics

来源：评论

学校读者我要写书评

暂无评论

Identifying gene-specific variations in biomedical text

引用

Journal of Bioinformatics and Computational Biology 2007年第6期5卷 1277-1296页

作者： Klinger, Roman Friedrich, Christoph M. Mevissen, Heinz Theodor Fluck, Juliane Hofmann-apitius, Martin Furlong, Laura I. Sanz, Ferran Department of Bioinformatics Fraunhofer Institute for Algorithms and Scientific Computing 53754 Sankt Augustin Schloss Birlinghoven Germany Research Unit on Biomedical Informatics (GRIB) IMIM UPF PRBB E-08003 Barcelona c/ Dr. Aiguader 88 Spain

The influence of genetic variations on diseases or cellular processes is the main focus of many investigations, and results of biomedical studies are often only accessible through scientific publications. Automatic extraction of this information requires recognition of the gene names and the accompanying allelic variant information. In a previous work, the OSIRIS system for the detection of allelic variation in text based on a query expansion approach was communicated. Challenges associated with this system are the relatively low recall for variation mentions and gene name recognition. To tackle this challenge, we integrate the ProMiner system developed for the recognition and normalization of gene and protein names with a conditional random field (CRF)-based recognition of variation terms in biomedical text. Following the newly developed normalization of variation entities, we can link textual entities to Single Nucleotide Polymorphism database (dbSNP) entries. The performance of this novel approach is evaluated, and improved results in comparison to state-of-the-art systems are reported. © 2007 Imperial College Press.

关键词： Conditional random field Named entity recognition Normalization Single nucleotide polymorphism SNP Variants

来源：评论

学校读者我要写书评

暂无评论

An Automatic Multi-Level Solver Switching Strategy for PEEC-Based EMC Simulation

An Automatic Multi-Level Solver Switching Strategy for PEEC-...

引用

EMC Zurich 2007 - 18th International Zurich Symposium on Electromagnetic Compatibility

作者： Tanja Clees Tatiana Samrowski Martin Ludwig Zitzmann Robert Weigel Fraunhofer Institute for Algorithms and Scientific Computing Sankt Augustin Germany BMW Group Munich Germany Institute for Electronics Engineering University of Erlangen Nuremberg Erlangen Germany

In this paper, we propose a new, efficient and robust automatic solver switching strategy, called alpha-SAMG, tailored to linear systems of equations arising in PEEC-based EMC simulation. The PEEC method (partial element equivalent circuit) is an approach for transforming conducting objects into linear networks with basic electrical elements. Such equivalent circuit models can be simulated by conventional circuit solvers such as SPICE (simulation program for integrated circuit emphasis) based on the MNA (modified nodal analysis) approach. By applying appropriate sparsification techniques, sparse PEEC matrices can be obtained, adequate for iterative solvers. By using multi-level approaches, linear complexity w.r.t. time and memory consumptions can be achieved in the best case. Due to the fact that properties of PEEC matrices can differ drastically, we developed the automatic solver switching strategy alpha-SAMG. Its efficiency for PEEC matrices is demonstrated for seven practically relevant benchmark cases by comparison against standard solvers. In particular, it is shown that alpha-SAMG provides a robust and fast solution strategy.

关键词： Electromagnetic compatibility Circuit simulation Integrated circuit modeling Robustness Equivalent circuits Analytical models Sparse matrices Linear systems Equations SPICE

来源：评论

学校读者我要写书评

暂无评论

Reconstruction of Chemical Molecules from Images

Reconstruction of Chemical Molecules from Images

引用

29th Annual International Conference of the IEEE Engineering in Medicine and Biology Society (EMBS 2007), vol.11

作者： Maria-Elena Algorri Marc Zimmermann Christoph M. Friedrich Santiago Akle Martin Hofmann-Apitius Department of Digital Systems Instituto Tecnologico Autonomo de Mexico Mexicali Mexico Department of Bioinformatics Fraunhofer Institute for Algorithms and Scientific Computing Sankt Augustin Germany

关键词： Image reconstruction Optical character recognition software Data mining Chemical products Image recognition Benchmark testing System testing Image databases Image converters Character recognition

来源：评论

学校读者我要写书评

暂无评论

Trust Issues in Shibboleth-Enabled Federated Grid Authentication and Authorization Infrastructures Supporting Multiple Grid Middleware

Trust Issues in Shibboleth-Enabled Federated Grid Authentica...

引用

IEEE International Conference on e-Science and Grid computing

作者： Christian Grimm Ralf Groeper Siegfried Makedanz Hans Pfeiffenberger Peter Gietz Martin Haase Michael Schiffers Wolfgang Ziegler RRZN Leibniz Universität Hannover Hanover Germany Alfred Wegener Institute Bremerhaven Germany DAASI International GmbH Tubingen Germany Ludwig-Maximilians University of Munich Munich Germany Institute for Algorithms and Scientific Computing Fraunhofer Gesellschaft e. V. Sankt Augustin Germany

In Germany's D-Grid project numerous grid communities are working together to develop a common overarching grid. One major aim of D-Grid is thus to integrate the existing grid deployments and make them interoperable. The major challenge in this endeavor lies in the heterogeneity of the current implementations: three grid middleware and different VO management approaches have to be orchestrated to achieve the intended interoperability. This paper presents some of the findings of the IVOM project regarding VO management technologies. Furthermore, options are discussed for making Shibboleth federations and VO management systems interoperable so that attributes from both sources can be used for authentication and authorization in grids. Finally two approaches, one using a so called "trust proxy" and one without trust proxying, are presented and support by current grid middleware is discussed.

关键词： Authentication Authorization Middleware Project management Technology management Grid computing scientific computing Communities IP networks Web services

来源：评论

学校读者我要写书评

暂无评论

建议与咨询留下您的常用邮箱和电话号码，以便我们向您反馈解决方案和替代方法

时间限定

文献类型

馆藏选择

核心期刊

语言

文献类型

帮助

文字说明：

检索规则说明：

检索范例：

分类表

所选分类

限定检索结果

文献类型

馆藏范围

日期分布

学科分类号

主题

机构

作者

语言

请选择保存的检索档案：

请选择收藏分类：

通借通还

建议与咨询 留下您的常用邮箱和电话号码，以便我们向您反馈解决方案和替代方法

时间限定

文献类型

馆藏选择

核心期刊

语言

文献类型

帮助

文字说明：

检索规则说明：

检索范例：

分类表

所选分类

限定检索结果

文献类型

馆藏范围

日期分布

学科分类号

主题

机构

作者

语言

请选择保存的检索档案： 新增检索档案 确定 取消

请选择收藏分类： 新增自定义分类 确定 取消

通借通还

建议与咨询留下您的常用邮箱和电话号码，以便我们向您反馈解决方案和替代方法

请选择保存的检索档案：

请选择收藏分类：