• Title/Summary/Keyword: User web interface

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Development of a Window Program for Searching CpG Island (CpG Island 검색용 윈도우 프로그램 개발)

  • Kim, Ki-Bong
    • Journal of Life Science
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    • v.18 no.8
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    • pp.1132-1139
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    • 2008
  • A CpG island is a short stretch of DNA in which the frequency of the CG dinucleotide is higher than other regions. CpG islands are present in the promoters and exonic regions of approximately $30{\sim}60$% of mammalian genes so they are useful markers for genes in organisms containing 5-methylcytosine in their genomes. Recent evidence supports the notion that the hypermethylation of CpG island, by silencing tumor suppressor genes, plays a major causal role in cancer, which has been described in almost every tumor types. In this respect, CpG island search by computational methods is very helpful for cancer research and computational promoter and gene predictions. I therefore developed a window program (called CpGi) on the basis of CpG island criteria defined by D. Takai and P. A. Jones. The program 'CpGi' was implemented in Visual C++ 6.0 and can determine the locations of CpG islands using diverse parameters (%GC, Obs (CpG)/Exp (CpG), window size, step size, gap value, # of CpG, length) specified by user. The analysis result of CpGi provides a graphical map of CpG islands and G+C% plot, where more detailed information on CpG island can be obtained through pop-up window. Two human contigs, i.e. AP00524 (from chromosome 22) and NT_029490.3 (from chromosome 21), were used to compare the performance of CpGi and two other public programs for the accuracy of search results. The two other programs used in the performance comparison are Emboss-CpGPlot and CpG Island Searcher that are web-based public CpG island search programs. The comparison result showed that CpGi is on a level with or outperforms Emboss-CpGPlot and CpG Island Searcher. Having a simple and easy-to-use user interface, CpGi would be a very useful tool for genome analysis and CpG island research. To obtain a copy of CpGi for academic use only, contact corresponding author.

Twitter Issue Tracking System by Topic Modeling Techniques (토픽 모델링을 이용한 트위터 이슈 트래킹 시스템)

  • Bae, Jung-Hwan;Han, Nam-Gi;Song, Min
    • Journal of Intelligence and Information Systems
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    • v.20 no.2
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    • pp.109-122
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    • 2014
  • People are nowadays creating a tremendous amount of data on Social Network Service (SNS). In particular, the incorporation of SNS into mobile devices has resulted in massive amounts of data generation, thereby greatly influencing society. This is an unmatched phenomenon in history, and now we live in the Age of Big Data. SNS Data is defined as a condition of Big Data where the amount of data (volume), data input and output speeds (velocity), and the variety of data types (variety) are satisfied. If someone intends to discover the trend of an issue in SNS Big Data, this information can be used as a new important source for the creation of new values because this information covers the whole of society. In this study, a Twitter Issue Tracking System (TITS) is designed and established to meet the needs of analyzing SNS Big Data. TITS extracts issues from Twitter texts and visualizes them on the web. The proposed system provides the following four functions: (1) Provide the topic keyword set that corresponds to daily ranking; (2) Visualize the daily time series graph of a topic for the duration of a month; (3) Provide the importance of a topic through a treemap based on the score system and frequency; (4) Visualize the daily time-series graph of keywords by searching the keyword; The present study analyzes the Big Data generated by SNS in real time. SNS Big Data analysis requires various natural language processing techniques, including the removal of stop words, and noun extraction for processing various unrefined forms of unstructured data. In addition, such analysis requires the latest big data technology to process rapidly a large amount of real-time data, such as the Hadoop distributed system or NoSQL, which is an alternative to relational database. We built TITS based on Hadoop to optimize the processing of big data because Hadoop is designed to scale up from single node computing to thousands of machines. Furthermore, we use MongoDB, which is classified as a NoSQL database. In addition, MongoDB is an open source platform, document-oriented database that provides high performance, high availability, and automatic scaling. Unlike existing relational database, there are no schema or tables with MongoDB, and its most important goal is that of data accessibility and data processing performance. In the Age of Big Data, the visualization of Big Data is more attractive to the Big Data community because it helps analysts to examine such data easily and clearly. Therefore, TITS uses the d3.js library as a visualization tool. This library is designed for the purpose of creating Data Driven Documents that bind document object model (DOM) and any data; the interaction between data is easy and useful for managing real-time data stream with smooth animation. In addition, TITS uses a bootstrap made of pre-configured plug-in style sheets and JavaScript libraries to build a web system. The TITS Graphical User Interface (GUI) is designed using these libraries, and it is capable of detecting issues on Twitter in an easy and intuitive manner. The proposed work demonstrates the superiority of our issue detection techniques by matching detected issues with corresponding online news articles. The contributions of the present study are threefold. First, we suggest an alternative approach to real-time big data analysis, which has become an extremely important issue. Second, we apply a topic modeling technique that is used in various research areas, including Library and Information Science (LIS). Based on this, we can confirm the utility of storytelling and time series analysis. Third, we develop a web-based system, and make the system available for the real-time discovery of topics. The present study conducted experiments with nearly 150 million tweets in Korea during March 2013.

Design and Implementation of MongoDB-based Unstructured Log Processing System over Cloud Computing Environment (클라우드 환경에서 MongoDB 기반의 비정형 로그 처리 시스템 설계 및 구현)

  • Kim, Myoungjin;Han, Seungho;Cui, Yun;Lee, Hanku
    • Journal of Internet Computing and Services
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    • v.14 no.6
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    • pp.71-84
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    • 2013
  • Log data, which record the multitude of information created when operating computer systems, are utilized in many processes, from carrying out computer system inspection and process optimization to providing customized user optimization. In this paper, we propose a MongoDB-based unstructured log processing system in a cloud environment for processing the massive amount of log data of banks. Most of the log data generated during banking operations come from handling a client's business. Therefore, in order to gather, store, categorize, and analyze the log data generated while processing the client's business, a separate log data processing system needs to be established. However, the realization of flexible storage expansion functions for processing a massive amount of unstructured log data and executing a considerable number of functions to categorize and analyze the stored unstructured log data is difficult in existing computer environments. Thus, in this study, we use cloud computing technology to realize a cloud-based log data processing system for processing unstructured log data that are difficult to process using the existing computing infrastructure's analysis tools and management system. The proposed system uses the IaaS (Infrastructure as a Service) cloud environment to provide a flexible expansion of computing resources and includes the ability to flexibly expand resources such as storage space and memory under conditions such as extended storage or rapid increase in log data. Moreover, to overcome the processing limits of the existing analysis tool when a real-time analysis of the aggregated unstructured log data is required, the proposed system includes a Hadoop-based analysis module for quick and reliable parallel-distributed processing of the massive amount of log data. Furthermore, because the HDFS (Hadoop Distributed File System) stores data by generating copies of the block units of the aggregated log data, the proposed system offers automatic restore functions for the system to continually operate after it recovers from a malfunction. Finally, by establishing a distributed database using the NoSQL-based Mongo DB, the proposed system provides methods of effectively processing unstructured log data. Relational databases such as the MySQL databases have complex schemas that are inappropriate for processing unstructured log data. Further, strict schemas like those of relational databases cannot expand nodes in the case wherein the stored data are distributed to various nodes when the amount of data rapidly increases. NoSQL does not provide the complex computations that relational databases may provide but can easily expand the database through node dispersion when the amount of data increases rapidly; it is a non-relational database with an appropriate structure for processing unstructured data. The data models of the NoSQL are usually classified as Key-Value, column-oriented, and document-oriented types. Of these, the representative document-oriented data model, MongoDB, which has a free schema structure, is used in the proposed system. MongoDB is introduced to the proposed system because it makes it easy to process unstructured log data through a flexible schema structure, facilitates flexible node expansion when the amount of data is rapidly increasing, and provides an Auto-Sharding function that automatically expands storage. The proposed system is composed of a log collector module, a log graph generator module, a MongoDB module, a Hadoop-based analysis module, and a MySQL module. When the log data generated over the entire client business process of each bank are sent to the cloud server, the log collector module collects and classifies data according to the type of log data and distributes it to the MongoDB module and the MySQL module. The log graph generator module generates the results of the log analysis of the MongoDB module, Hadoop-based analysis module, and the MySQL module per analysis time and type of the aggregated log data, and provides them to the user through a web interface. Log data that require a real-time log data analysis are stored in the MySQL module and provided real-time by the log graph generator module. The aggregated log data per unit time are stored in the MongoDB module and plotted in a graph according to the user's various analysis conditions. The aggregated log data in the MongoDB module are parallel-distributed and processed by the Hadoop-based analysis module. A comparative evaluation is carried out against a log data processing system that uses only MySQL for inserting log data and estimating query performance; this evaluation proves the proposed system's superiority. Moreover, an optimal chunk size is confirmed through the log data insert performance evaluation of MongoDB for various chunk sizes.