• 한국생물정보학회:학술대회논문집
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• 한국생물정보시스템생물학회 2004년도 The 3rd Annual Conference for The Korean Society for Bioinformatics Association of Asian Societies for Bioinformatics 2004 Symposium
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• pp.13-20
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• 2004

Grid system has the potential to resolve the current need of bioinformatics for super-computing environment inexpensively. There are already several Grid applications of bioinformatics tools. To solve the real-world bioinformatics problems, however, the various integration of each tool is necessary in addition to the implementation of more basic tools. Workflow based problem solving environment can be the efficient solution for this type of software development. There are still heavy overhead, however, to develop and implement workflow model on current Grid system. He re we propose a model of simple problem solving environment that enables component based workflow design of integrated bioinformatics applications on Grid environment by using Condor functionalities. We realized this model for practical bioinformatics solutions of a genome sequence analysis and a comparative genome analysis. We implemented necessary bioinformatics tools and interfacing tools as the components, and combine them in the workflow model of each solution by using the tools presented in Condor.

• International Journal of Fuzzy Logic and Intelligent Systems
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• 제3권2호
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• pp.133-137
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• 2003

Various bioinformatics tools for biological data processing have been developed and most of them are available in public. Most bioinformatics works are carried out by a composite application of those tools. Several integration approaches have been proposed for easy use of the tools. This paper proposes a new multi agent system to integrate bioinformatics tools in the perspective of workflow since the composite applications of tools can be regarded as workflows. For the easy integration, the proposed system employs wrapper agents for existing tools, uses XML-based messages in the inter-agent communication, and agents are supposed to extract necessary information from the received messages. This allows new tools to be easily added on the integration framework. The proposed method allows various control structures in workflow definition and provides the progress monitoring capability of the on-going workflows. In particular, agents in this system have the rule-based architecture which allows the defined rule set to be a special role agent. This feature provides fast and flexible agent development to aid in managing the complexity of bioinformatics application. This system has been partially implemented and has been proven to be a viable implementation for workflow-based bioinformatics tool integration.

• Interdisciplinary Bio Central
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• 제3권3호
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• pp.12.1-12.3
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• 2011

Bioinformatics tools and databases are useful for understanding and processing various biological data. Numerous resources are being published each year. It is not a trivial task to find up-to-date relevant tools and databases. Moreover, no server is available to provide comprehensive coverage on bioinformatics resources in all biological fields. Here, we present a directory server called IntoPub that provides information on web resources. First, we downloaded XML-formatted abstracts containing web URLs from the NCBI PubMed database by using 'ESearch-EFetch' function in the NCBI E-utilities. The information is obtained from abstracts in the PubMed by extracting 'www' or 'http' prefixes. Then, we cu-rate the downloaded abstracts both in automatic and manual fashion. As of July 2011, the IntoPub database has 12,118 abstracts containing web URLs from 174 journals. Our anal-ysis shows that the number of abstracts containing web resources has increased signifi-cantly every year. The server has been tested by many biologists from several countries to get opinion on user satisfaction, usefulness, practicability, and ease of use since January 2010. In the IntoPub web server, users can easily find relevant bioinformatics resources, as compared to searching in PubMed. IntoPub will continue to update and incorporate new web resources from PubMed and other literature databases. IntoPub, available at http://into.kobic.re.kr/, is updated every day.

• 한국지능시스템학회:학술대회논문집
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• 한국퍼지및지능시스템학회 2003년도 ISIS 2003
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• pp.94-97
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• 2003

Various bioinformatics tools for biological data processing have been developed and most of them are available in public. Most bioinformatics works are carried out by a composite application of those tools. Several integration approaches have been proposed for easy use of the tools. This paper proposes a new multiagent system architecture to integrate bioinformatics tools in the perspective of workflow since the composite applications of tools can be regarded as workflows. For the easy integration, the proposed architecture employs wrapper agents for existing tools, uses XML-based messages in the inter-agent communication, and agents are supposed to extract necessary information from the received messages. This allows new tools to be easily added on the integration framework. The proposed method allows various control structures in workflow definition and provides the progress monitoring capability of the on-going workflows. We implemented a prototype system of the proposed architecture for annotating the genes of a bacterium called Sphingomonas Chungbukensis DJ77.

• Genomics & Informatics
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• 제11권3호
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• pp.102-113
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• 2013

Metagenomics has become one of the indispensable tools in microbial ecology for the last few decades, and a new revolution in metagenomic studies is now about to begin, with the help of recent advances of sequencing techniques. The massive data production and substantial cost reduction in next-generation sequencing have led to the rapid growth of metagenomic research both quantitatively and qualitatively. It is evident that metagenomics will be a standard tool for studying the diversity and function of microbes in the near future, as fingerprinting methods did previously. As the speed of data accumulation is accelerating, bioinformatic tools and associated databases for handling those datasets have become more urgent and necessary. To facilitate the bioinformatics analysis of metagenomic data, we review some recent tools and databases that are used widely in this field and give insights into the current challenges and future of metagenomics from a bioinformatics perspective.

• Genomics & Informatics
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• 제5권4호
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• pp.200-202
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• 2007

For the past several years, we have built various tools for automatic construction of biopathways to help biological experts, especially in the field of agriculture. We integrated several systems for constructing web applications for analyzing biological pathway information for agricultural species, constructing optimized pathway maps. In addition to building web applications for agricultural pathway information, we developed several stand-alone software tools, which are publicly downloadable under proper license agreements.

• 한국콘텐츠학회:학술대회논문집
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• 한국콘텐츠학회 2007년도 추계 종합학술대회 논문집
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• pp.3-6
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• 2007

한국과학기술정보연구원(KISTI) CCBB(Center for Computational Biology & Bioinformatics) 웹사이트에서는 IT 기반의 생명정보 인프라 구축을 위해 생명정보 콘텐트(DB, 분석도구) 21종을 구축 서비스하고 있다. 또한, 국내 생명정보 연구개발 지원 및 인프라 조성을 위한 업무를 수행하고 있다. 하지만 CCBB에 대한 인식이 널리 확산되어 있지 않아 CCBB에서 구축하고 개발된 생명정보 콘텐트가 활발히 이용되지 못하고 있는 실정이다. 따라서 생명과학 분야의 연구자를 대상으로 이용자조사를 실시하였다. 조사내용은 생명정보 데이터 베이스 및 분석도구 이용에 관한 내용과 생명과학 연구학술정보 네트워크(BioInfoNet)에 관한 내용으로 구성하였다. 설문조사를 통해 나타난 결과는 정리 분석한 후 이용자들이 필요로 하는 데이터베이스, 분석도구 등 생명정보 인프라를 제공하는데 활용될 것이다.

• 생명과학회지
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• 제25권3호
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• pp.357-367
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• 2015

매우 빠른 속도로 발전하고 있는 차세대 염기서열 분석 플랫폼과 최신 생물정보학적 분석도구들로 말미암아, 1,000달러 이하의 가격으로 인간 유전체 염기서열을 해독하고자 하는 궁극적인 목표가 조만간 곧 실현될 수 있을 것 같다. 차세대 염기서열 분석 분야의 급속한 기술적 진전은 NGS 데이터의 분석과 관리를 위한 통계적 방법과 생물정보학적 분석도구들에 대한 수요를 꾸준히 증대시키고 있다. NGS 플랫폼이 상용화되어 쓰이기 시작한 초창기부터, NGS 데이터를 분석하고 해석하거나, 가시화 해주는 다수의 응용프로그램이나 도구들이 개발되어 활용되어 왔다. 그러나, NGS 데이터의 엄청난 범람으로 데이터 저장, 데이터 분석 및 관리 등에 있어서 해결해야 할 많은 문제들이 부각되고 있다. NGS 데이터 분석은 단편서열과 참조서열간의 서열정렬, 염기식별, 다형성 발견, 쌍단편 서열이나 비쌍단편 서열 등을 이용한 어셈블리 작업, 구조변이 발견, 유전체 브라우징 등을 본질적으로 포함한다. 본 논문은 주요 차세대 염기서열 결정기술과 NGS 데이터 분석을 위한 생물정보학적 분석도구들에 대해 개관적으로 소개하고자 한다.

• Journal of Pharmaceutical Investigation
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• 제34권1호
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• pp.73-79
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• 2004

The union of information-technology and biology presents great possibilities to both applications of bio-information and development of science and technology. Also, meaningful analysis of bio-information brings about a new innovation in the field of bio-market with the advent and growth of bioinformatics. Hence, bioinformatics is the most import aspect for establishing a science-technology-oriented society in the $21^{st}$ century. This article provides trends in current state of bioinformatics. Technological development of bioinformatics for the rapid growth of bio-industry means that using bioinformatics, a biologist can process and store enormous amount of data such as current Human Genome Project and future data in the field of biology. We have manly looked at the tends of bio-information, databases and mining tools that are generally used, and strategies and directions for the future.

• Genomics & Informatics
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• 제20권1호
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• pp.3.1-3.10
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• 2022

The recent development of whole-genome sequencing technologies paved the way for understanding the genomes of microorganisms. Every whole-genome sequencing (WGS) project requires a considerable cost and a massive effort to address the questions at hand. The final step of WGS is data analysis. The analysis of whole-genome sequence is dependent on highly sophisticated bioinformatics tools that the research personal have to buy. However, many laboratories and research institutions do not have the bioinformatics capabilities to analyze the genomic data and therefore, are unable to take maximum advantage of whole-genome sequencing. In this aspect, this study provides a guide for research personals on a set of bioinformatics tools available online that can be used to analyze whole-genome sequence data of bacterial genomes. The web interfaces described here have many advantages and, in most cases exempting the need for costly analysis tools and intensive computing resources.