2011 IEEE Seventh International Conference on e-Science Workshops最新文献

Watershed Reanalysis: Towards a National Strategy for Model-Data Integration 分水岭再分析:迈向模型-数据整合的国家战略

2011 IEEE Seventh International Conference on e-Science Workshops Pub Date : 2011-12-05 DOI: 10.1109/ESCIENCEW.2011.32

C. Duffy, Lorne Leonard, G. Bhatt, Xuan Yu, C. Lee Giles

引用次数: 7

Data Decomposition in Biomedical e-Science Applications 生物医学电子科学应用中的数据分解

2011 IEEE Seventh International Conference on e-Science Workshops Pub Date : 2011-12-05 DOI: 10.1109/eScienceW.2011.7

Yassene Mohammed, Shayan Shahand, V. Korkhov, Angela C. M. Luyf, B. V. Schaik, M. Caan, A. V. Kampen, Magnus Palmblad, S. Olabarriaga

{"title":"Data Decomposition in Biomedical e-Science Applications","authors":"Yassene Mohammed, Shayan Shahand, V. Korkhov, Angela C. M. Luyf, B. V. Schaik, M. Caan, A. V. Kampen, Magnus Palmblad, S. Olabarriaga","doi":"10.1109/eScienceW.2011.7","DOIUrl":"https://doi.org/10.1109/eScienceW.2011.7","url":null,"abstract":"As the focus of e-Science is moving toward the forth paradigm and data intensive science, data access remains dependent on the architecture of the used e-Science infrastructure. Such architecture is in general job-driven, i.e., a (grid) job is a sequence of commands that run on the same worker node. Making use of the infrastructure involves having a parallelized application. This is done foremost by data decomposition. In general practice of parallel programming, data decomposition depends on the programmer's experience and knowledge about the used data and the algorithm/application. On the other hand, data mining scientists have an established foundation for data decomposition, automatic decomposition methods are already in use, methodologies and patterns are defined. Our experience in porting biomedical applications to the Dutch e-Science infrastructure shows that the used data decomposition to gain parallelism fit to some degree a subgroup of the data mining decomposition patterns, i.e., object set decomposition. In this paper we discuss porting three biomedical packages to a grid computing environment, two for medical imaging and one for DNA sequencing. We show how the data access of the applications was reengineered around the executables to make use of the parallel capacity of e-Science infrastructure.","PeriodicalId":267737,"journal":{"name":"2011 IEEE Seventh International Conference on e-Science Workshops","volume":"341 1","pages":"0"},"PeriodicalIF":0.0,"publicationDate":"2011-12-05","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"124213989","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

引用次数: 3

Effective Computational Method for Evaluation of Dynamic Elecrostatic Effects of Explicit Solvent and Membrane Molecules from Molecular Dynamics Simulations 从分子动力学模拟中评价溶剂和膜分子动态静电效应的有效计算方法

2011 IEEE Seventh International Conference on e-Science Workshops Pub Date : 2011-12-05 DOI: 10.1109/eScienceW.2011.18

Y. Yonezawa

{"title":"Effective Computational Method for Evaluation of Dynamic Elecrostatic Effects of Explicit Solvent and Membrane Molecules from Molecular Dynamics Simulations","authors":"Y. Yonezawa","doi":"10.1109/eScienceW.2011.18","DOIUrl":"https://doi.org/10.1109/eScienceW.2011.18","url":null,"abstract":"Knowledge of the electronic structures of local functional sites of proteins sheds light into their fundamental mechanisms of enzymatic reaction and processes related to electronic state. Although the dynamic effects due to solvent or membrane molecules surrounding the protein are indispensable for an accurate analysis, in current methods they have been approximated by a continuum model with polarized material, where a phenomenological and unreliable parameter, the dielectric constant, is always required. We have developed a new algorithm to reproduce an average field due to the solvent and membrane molecules, which are calculated from the long trajectory of a classical molecular dynamics simulation for a membrane protein-solvent system, by several thousands of pseudo-charges and dipoles on a closed surface surrounding a target quantum mechanical (QM) region. Since the dynamic effects are represented only by \"static\" pseudo-charges and dipoles, the QM calculation is necessarily done only once. We applied this algorithm to the photosynthetic reaction center of Rhodobacter sphaeroides with explicit all-atomic models of the solvent and membrane molecules. It is possible that the electronic structures of its ground state and excited state can be calculated with those microscopic \"reaction field\" effects.","PeriodicalId":267737,"journal":{"name":"2011 IEEE Seventh International Conference on e-Science Workshops","volume":"108 1","pages":"0"},"PeriodicalIF":0.0,"publicationDate":"2011-12-05","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"128159764","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

引用次数: 0

Assessment of Resource Quality for Service Level Agreements in Life Science Grids 生命科学网格中服务水平协议的资源质量评估

2011 IEEE Seventh International Conference on e-Science Workshops Pub Date : 2011-12-05 DOI: 10.1109/ESCIENCEW.2011.17

Tibor K´lm´n

{"title":"Assessment of Resource Quality for Service Level Agreements in Life Science Grids","authors":"Tibor K´lm´n","doi":"10.1109/ESCIENCEW.2011.17","DOIUrl":"https://doi.org/10.1109/ESCIENCEW.2011.17","url":null,"abstract":"This article focuses on measuring, describing, monitoring and publishing the quality and performance of grid resources. Life science communities can employ Service Level Agreements (SLAs) with their resource providers to ensure the delivery of services. For this, it is important for both the life science communities and their providers to understand and quantify the performance and service quality of different grid environments. However, measuring service quality in grid infrastructures utilizing different middle wares, as in the German Grid Initiative, is a complex problem. We describe the state of quality metrics which are currently used by the German life science communities MediGRID, Services@MediGRID and PneumoGrid. We also identify further quality metrics for defining and monitoring grid resource quality in D-Grid. It is important to publish and exchange the quality information by grid information systems, which are the entry points to grid services. Therefore, we also present how quality information can be handled by the GLUE v2.0 Schema, which is the upcoming standard data model used by grid information systems. For measuring and monitoring the quality metrics in multi-middleware environments two approaches are discussed. The first approach extracts quality information from an external benchmarking system and loads iit to the grid information systems. The second solution targets life science communities that do not utilize legacy benchmarking systems, but operate traditional monitoring systems, like Nagios.","PeriodicalId":267737,"journal":{"name":"2011 IEEE Seventh International Conference on e-Science Workshops","volume":"10 1","pages":"0"},"PeriodicalIF":0.0,"publicationDate":"2011-12-05","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"121875568","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

引用次数: 0

Gaming for (Citizen) Science: Exploring Motivation and Data Quality in the Context of Crowdsourced Science through the Design and Evaluation of a Social-Computational System (公民)科学的游戏:通过社会计算系统的设计和评估，探索众包科学背景下的动机和数据质量

2011 IEEE Seventh International Conference on e-Science Workshops Pub Date : 2011-12-05 DOI: 10.1109/ESCIENCEW.2011.14

Nathan R. Prestopnik, Kevin Crowston

引用次数: 64

A Flexible Database-Centric Platform for Citizen Science Data Capture 一个灵活的以数据库为中心的公民科学数据捕获平台

2011 IEEE Seventh International Conference on e-Science Workshops Pub Date : 2011-12-05 DOI: 10.1109/ESCIENCEW.2011.15

C. Ellul, L. Francis, M. Haklay

{"title":"A Flexible Database-Centric Platform for Citizen Science Data Capture","authors":"C. Ellul, L. Francis, M. Haklay","doi":"10.1109/ESCIENCEW.2011.15","DOIUrl":"https://doi.org/10.1109/ESCIENCEW.2011.15","url":null,"abstract":"The paper describes a platform developed by the Extreme Citizen Science (ExCiteS) group at University College London over the past five years to facilitate online data capture by Citizen Scientists in the context of community science, where local environmental problems are monitored. Responding to user needs, the platform has been developed to be as flexible as possible in terms of the types of data that can be captured -- these currently include numbers, text, video, photography, pull-down lists, multiple selection lists and so forth. Live data feeds and links to social networking such as twitter have also been incorporated. This platform is database-centric, and thus allows capture and storage of data from multiple devices (currently Web and mobile) in one central location. All map-based data is captured and held in native spatial data format inside the database. To support Citizen Science activity, the system has been designed to allow new projects to be added without the requirement for additional development (programming), and an administration tool developed to support this task. Each project is allocated custom themes depending on the project requirements and a variety of 'skins' can be configured to give the website a different appearance in each case. The platform is currently used by over 20 different groups within the United Kingdom -- though mostly for more social and perceptual data collection, rather than scientific. After demonstrating its use in an urban noise study, it is now adapted to use in air pollution studies. An extension to mobile devices (Android) is also underdevelopment.","PeriodicalId":267737,"journal":{"name":"2011 IEEE Seventh International Conference on e-Science Workshops","volume":"89 1","pages":"0"},"PeriodicalIF":0.0,"publicationDate":"2011-12-05","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"114225097","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

引用次数: 10

Mechanisms for Data Quality and Validation in Citizen Science 公民科学中的数据质量和验证机制

2011 IEEE Seventh International Conference on e-Science Workshops Pub Date : 2011-12-05 DOI: 10.1109/ESCIENCEW.2011.27

A. Wiggins, Greg Newman, R. Stevenson, Kevin Crowston

引用次数: 188

Accelerating 3D Protein Modeling Using Cloud Computing: Using Rosetta as a Service on the IBM SmartCloud 使用云计算加速3D蛋白质建模:在IBM SmartCloud上使用Rosetta即服务

2011 IEEE Seventh International Conference on e-Science Workshops Pub Date : 2011-12-05 DOI: 10.1109/eScienceW.2011.12

P. Kunszt, L. Malmström, Nicola Fantini, Wibke Sudholt, M. Lautenschlager, Roland Reifler, Stefan Ruckstuhl

引用次数: 3

A Type System for High Performance Communication and Computation 一种高性能通信与计算型系统

2011 IEEE Seventh International Conference on e-Science Workshops Pub Date : 2011-12-05 DOI: 10.1109/eScienceW.2011.16

G. Eisenhauer, M. Wolf, H. Abbasi, S. Klasky, K. Schwan

{"title":"A Type System for High Performance Communication and Computation","authors":"G. Eisenhauer, M. Wolf, H. Abbasi, S. Klasky, K. Schwan","doi":"10.1109/eScienceW.2011.16","DOIUrl":"https://doi.org/10.1109/eScienceW.2011.16","url":null,"abstract":"The manner in which data is represented, accessed and transmitted has an affect upon the efficiency of any computing system. In the domain of high performance computing, traditional frameworks like MPI have relied upon a relatively static type system with a high degree of a priori knowledge shared among the participants. However, modern scientific computing is increasingly distributed and dynamic, requiring the ability to dynamically create multi-platform workflows, to move processing to data, and to perform both in situ and streaming data analysis. Traditional approaches to data type description and communication in middleware, which typically either require a priori agreement on data types, or resort to highly inefficient representations like XML, are insufficient for the new domain of dynamic science. This paper describes a different approach, using FFS, a middleware library that implements efficient manipulation of application-level data. FFS provides for highly efficient binary data communication, XML-like examination of unknown data, and both third-party and in situ data processing via dynamic code generation. All of these capabilities are fully dynamic at run-time, without requiring a priori agreements or knowledge of the exact form of the data being communicated or analyzed.","PeriodicalId":267737,"journal":{"name":"2011 IEEE Seventh International Conference on e-Science Workshops","volume":"17 1","pages":"0"},"PeriodicalIF":0.0,"publicationDate":"2011-12-05","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"126192155","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

引用次数: 17

Taxonomy of Multiscale Computing Communities 多尺度计算社区分类法

2011 IEEE Seventh International Conference on e-Science Workshops Pub Date : 2011-12-05 DOI: 10.1109/eScienceW.2011.11

D. Groen, S. Zasada, P. Coveney

引用次数: 10