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Client-server architecture for pre and post-processing of real problems involving two-dimensional generalized coordinates

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INTERNATIONAL JOURNAL OF web INFORMATION SYSTEMS 2015年第2期11卷 226-245页

作者： Vilas Boas, Jose Luiz Matsunaga, Fabio Takeshi Lopes Romeiro, Neyva Maria Brancher, Jacques Duilio Univ Estadual Londrina Dept Comp Sci Londrina Brazil Univ Estadual Londrina Dept Math Londrina Brazil

Purpose - The aim of this paper is to propose a web environment for pre-processing and post-processing for 2D problems in generalized coordinate systems. Design/methodology/approach - The system consists of a web service for client-server communication, a database for user information, simulation requests and results storage, a module of (for) calculation processing (front-end) and a graphical interface for visualization of discretized mesh (back-end). Findings - The web system was able to model real problems and situations, where the user can describe the problem or upload a geometry file descriptor, generated from computer graphics software. The web system, programmed for finite difference solutions, was able to generate a mesh from other complex methods, such as finite elements method, adapting it to the proposed web system, respecting the finite difference mesh structure. Research limitations/implications - The proposed web system is limited to solve partial differential equations by finite difference discretization. We need to study about refinement and parameters adaptations to solve partial differential equations simulated with other methods. Practical implications - The web system includes implications for the development of a powerful real problems simulator, which is useful for computational physics researchers and engineers. The web system uses several technologies, such as Primefaces, JavaScript, JQuery and HTML, to provide an interactive user interface. Originality/value - The main contribution of this work is the availability of a generic web architecture for including other types of coordinate systems and to solve others partial differential equations. Moreover, this paper presents an extended version of the work presented in ICCSA 2014.

关键词： Advanced web applications Mobile computing for the Internet web databases web data integration web architecture

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High-Throughput In Situ Hybridization: Systematical Production of Gene Expression Data and Beyond

High-Throughput In Situ Hybridization: Systematical Producti...

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作者： Lars Geffers Gregor Eichele

A plethora of modern-day techniques allows the detailed characterization of the transcriptome on a quantitative level. Analyses, based on techniques such as cDNA microarrays or RNA-seq (whole transcriptome shotgun sequencing), are usually genome wide in scope and readily detect small changes in gene expression levels across different biological samples. However, when it comes to spatial localization of gene expression within the context of complex tissues, traditional methods of in situ hybridization remain unparalleled with regard to their cellular resolution. Here we review methods that extend classical in situ hybridization protocols and techniques to the special needs of high-throughput (HT) studies and which can be readily scaled up to a genomic level to cover organs or even whole organisms in great detail. Moreover, we discuss suitable HT instrumentation and address postproduction issues typically arising with HT pipelines such as annotation of expression data and database organization. less

关键词： In Situ Hybridization Functional Genomics Gene Expression Analysis RNA-seq PCR Nucleic Acid Hybridization Microarray Ovis aries Annotation web databases Anti-DIG

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Identifying and determining SPARQL endpoint characteristics

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INTERNATIONAL JOURNAL OF web INFORMATION SYSTEMS 2014年第3期10卷 226-+页

作者： Lorey, Johannes Hasso Plattner Inst Informat Syst Grp Potsdam Germany

Purpose - The purpose of this study is to introduce several metrics that enable universal and fine-grained characterization of arbitrary Linked Data repositories. Publicly accessible SPARQL endpoints contain vast amounts of knowledge from a large variety of domains. However, oftentimes these endpoints are not configured to process specific workloads as efficiently as possible. Assisting users in leveraging SPARQL endpoints requires insight into functional and non-functional properties of these knowledge bases. Design/methodology/approach - This study presents comprehensive approaches for deriving these metrics. More specifically, the study utilizes concrete SPARQL queries to determine corresponding values. Furthermore, it validates and discusses the introduced metrics through extensive evaluation on real-world SPARQL endpoints. Findings - The evaluation determined that endpoints exhibit different characteristics. While it comes as no surprise that latency and throughput are influenced by the network infrastructure, the costs for join operations depend on a number of factors that are not obvious to a data consumer. Moreover, as the author discusses mean, median and upper quartile values, it was found both endpoints behaving consistently as well as repositories offering varying levels of performance. Originality/value - On the one hand, the contribution of the authors work lies in assisting data consumers in evaluation of the quality of service of publicly available SPARQL endpoints. On the other hand, the performance metrics introduced in this study can also be considered as additional input features for distributed query processing frameworks. Moreover, the author provides a universal means for discerning characteristics of different SPARQL endpoints without the need of (synthetic or real-world) query workloads.

关键词： Standards Advanced web applications Internet quality of service web applications performance web semantics architectures web databases Applications

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Automatic Structured web databases Classification

Automatic Structured Web Databases Classification

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2010 IEEE International Conference on Intelligent Computing and Intelligent Systems(2010 IEEE 智能计算与智能系统国际会议 ICIS 2010)

作者： XiaoJun Cui ZhongSheng Ren Le Xu HongYu Xiao Wenzhou Vocational College of Science and Technology Wenzhou China State Key Laboratory of Software College of Mathematics and Computer Science Fujian Normal University Fuzhou China Department of Information and Technology Wenzhou Vocational College of Science and Technology Wenzho

The growing structured web databases on the web, making large-scale Deep web data integration faces enormous challenges. Organizing such structured web databases into a hierarchy directory tree is one of critical step towards the large-scale integration of Deep web. In this paper, a method for automatic classification of web database is addressed. Firstly, the method for calculating the semantic similarities among the web databases based on their interface schemas is proposed and be translated to the problem of extended optimal matching for bipartite graph. Then based on the achieved similarity matrix, an agglomerative hierarchical clustering algorithm is proposed, which can organize the web databases into a hierarchy tree automatically. Theoretical analysis and experimental results show that the method is efficient.

关键词： web databases interface schema bipartite graph matching hierarchical clustering

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Exploration and Mining of web Repositories 14

Exploration and Mining of Web Repositories

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7th ACM International Conference on web Search and Data Mining (WSDM)

作者： Zhang, Nan Das, Gautam George Washington Univ Washington DC 20052 USA Univ Texas Arlington Arlington TX 76019 USA

ISBN: (纸本)9781450323512

With the proliferation of very large data repositories hidden behind web interfaces, e.g., keyword search, form-like search and hierarchical/graph-based browsing interfaces for ***, ***, etc., efficient ways of searching, exploring and/or mining such web data are of increasing importance. There are two key challenges facing these tasks: how to properly understand web interfaces, and how to bypass the interface restrictions. In this tutorial, we start with a general overview of web search and data mining, including various exciting applications enabled by the effective search, exploration, and mining of web repositories. Then, we focus on the fundamental developments in the field, including web interface understanding, crawling, sampling, and data analytics over web repositories with various types of interfaces. We also discuss the potential changes required for query processing, data mining and machine learning algorithms to be applied to web data. Our goal is two-fold: one is to promote the awareness of existing web data search/exploration/mining techniques among all web researchers who are interested in leveraging web data, and the other is to encourage researchers, especially those who have not previously worked in web search and mining before, to initiate their own research in these exciting areas.

关键词： web Repositories web databases Deep web Data Analytics

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BayesWipe: A Multimodal System for Data Cleaning and Consistent Query Answering on Structured BigData 2

BayesWipe: A Multimodal System for Data Cleaning and Consist...

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IEEE International Conference on Big Data

作者： De, Sushovan Hu, Yuheng Chen, Yi Kambhampati, Subbarao Arizona State Univ Dept Comp Sci & Engn Tempe AZ 85281 USA New Jersey Inst Technol Sch Management Newark NJ 07102 USA

ISBN: (纸本)9781479956661

Recent efforts in data cleaning of structured data have focused exclusively on problems like data deduplication, record matching, and data standardization;none of these focus on fixing incorrect attribute values in tuples. Correcting values in tuples is typically performed by a minimum cost repair of tuples that violate static constraints like CFDs (which have to be provided by domain experts, or learned from a clean sample of the database). In this paper, we provide a method for correcting individual attribute values in a structured database using a Bayesian generative model and a statistical error model learned from the noisy database directly. We thus avoid the necessity for a domain expert or clean master data. We also show how to efficiently perform consistent query answering using this model over a dirty database, in case write permissions to the database are unavailable. We evaluate our methods over both synthetic and real data.

关键词： databases web databases data cleaning query rewriting uncertainty

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A Review of “Linked Data for Libraries, Archives and Museums: How to Clean, Link and Publish Your Metadata.”

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Journal of Electronic Resources Librarianship 2014年第4期26卷 308-309页

作者： Paul Martinez

Click to increase image sizeClick to decrease image size

关键词： LINKED data (Semantic web) web databases NONFICTION

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Behavior analysis methods for Twitter users based on transitions in posting activities

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INTERNATIONAL JOURNAL OF web INFORMATION SYSTEMS 2014年第4期10卷 363-+页

作者： Yamaguchi, Yutaro Yamamoto, Shuhei Satoh, Tetsuji Univ Tsukuba Grad Sch Lib Informat & Media Studies Tsukuba Ibaraki Japan Univ Tsukuba Fac Lib Informat & Media Studies Tsukuba Ibaraki Japan

Purpose - The purpose of this paper is to activate latent users posts by modeling user behaviors by a transition of clusters that represent particular posting activities. Twitter has rapidly spread and become an easy and convenient microblog that enables users to exchange instant text messages called tweets. There are so many latent users whose posting activities have decreased. Design/methodology/approach - Under this model, two kinds of time-series analysis methods are proposed to clarify the lifecycles of Twitter users. In the first one, all users belong to a cluster consisting of several features at individual time slots and move among the clusters in a time series. In the second one, the posting activities of Twitter users are analyzed by the amount of tweets that vary with time. Findings - This sophisticated evaluation using a large actual tweet-set demonstrated the proposed methods effectiveness. The authors found a big difference in the state transition diagrams between long- and short-term users. Analysis of short-term users introduces effective knowledge for encouraging continued Twitter use. Originality/value - An the efficient user behavior model, which describes transitions of posting activities, is proposed. Two kinds of time longitudinal analysis method are evaluated using a large amount of actual tweets.

关键词： Communities on the web web mining web databases

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Probabilistic web Data Management

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WORLD WIDE web-INTERNET AND web INFORMATION SYSTEMS 2013年第3期16卷 271-272页

作者： Chen, Lei Ilyas, Ihab Re, Christopher Zhou, Xiaofang Hong Kong Univ Sci & Technol Dept Comp Sci & Engn Kowloon Hong Kong Peoples R China

With the development of web 2.0 technology, enormous data are generated every day. Among these data, there exist quite a lot uncertainty due to careless data entry, incomplete information, and inconsistency among different data description. Although significant effort has been paid to find effective and efficient solutions for managing and mining general uncertain data, little attention is paid to manage uncertain data on the web. This special issue is proposed to attract research attempts on handling uncertainty of the web data. This special issue has attracted 12 submissions, after two rounds of very careful reviews by domain experts, we accepted three excellent papers. These three papers present new ideas to address issues on Probabilistic web Data Management.

关键词： web development XML (Document markup language) web databases

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The 2013 Plant and Cell Physiology Database Issue

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PLANT AND CELL PHYSIOLOGY 2013年第2期54卷 169-170页

作者： Obayashi, Takeshi Yano, Kentaro Tohoku Univ Sch Informat Sci Sendai Miyagi 980 Japan Meiji Univ Sch Agr Tokyo 101 Japan

We are pleased to announce the publication of this third Database Issue of Plant and Cell Physiology (PCP). It contains four new databases and seven updated databases (Tables 1, 2). Our aim with this issue is to provide a forum for discussion of bioinformatics research, in particular the development and maintenance of the infrastructure of web databases for plant science (Matsuoka and Yano 2010). The databases described in this issue cover a broad range of omics topics. The genome and transcriptome databases permit management of the ood of data from recent high-throughput sequencers, and have been rapidly extended to apply to non-model plants. On the other hand, metabolome and phenome data still require databases and web tools to store, annotate and compare the data. In the following paragraphs, we briey introduce the 11 databases in this issue and broadly describe their functions.

关键词： web databases MODEL PLANTS Debates INFRASTRUCTURE publications Genome sequencer Database Cell Physiological Phenomena

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