• Proceedings of the Korean Society for Bioinformatics Conference
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• 2004.11a
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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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• v.3 no.2
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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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• v.3 no.3
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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.

• Proceedings of the Korean Institute of Intelligent Systems Conference
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• 2003.09a
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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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• v.11 no.3
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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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• v.5 no.4
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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.

• Proceedings of the Korea Contents Association Conference
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• 2007.11a
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• pp.3-6
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• 2007

KISTI(Korea Institute of Science & Technology Information) CCBB(Center for Computational Biology and Bioinformatics) Website has been providing bioinformatics contents(databases and analysis tools) services to construct IT-based bioinformatics infrastructure. It also carries out the services to support domestic bioinformatics R&D activity and to construct the infrastructure. But, these services are not actively available because this CCBB website is not wellknown to users. Therefore, we performed the user survey for the researchers who are studying in the field of biological science. The items of this survey consist of subjects on bioinformatics databases, analysis tools and BioInfoNet. After the user survey is rearranged and analyzed, the result of survey will be used to provide the good service to the users who are need of bioinformatics infrastructure such as databases and analysis tools etc.

• Journal of Life Science
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• v.25 no.3
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• pp.357-367
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• 2015

With the ongoing development of next-generation sequencing (NGS) platforms and advancements in the latest bioinformatics tools at an unprecedented pace, the ultimate goal of sequencing the human genome for less than $1,000 can be feasible in the near future. The rapid technological advances in NGS have brought about increasing demands for statistical methods and bioinformatics tools for the analysis and management of NGS data. Even in the early stages of the commercial availability of NGS platforms, a large number of applications or tools already existed for analyzing, interpreting, and visualizing NGS data. However, the availability of this plethora of NGS data presents a significant challenge for storage, analyses, and data management. Intrinsically, the analysis of NGS data includes the alignment of sequence reads to a reference, base-calling, and/or polymorphism detection, de novo assembly from paired or unpaired reads, structural variant detection, and genome browsing. While the NGS technologies have allowed a massive increase in available raw sequence data, a number of new informatics challenges and difficulties must be addressed to improve the current state and fulfill the promise of genome research. This review aims to provide an overview of major NGS technologies and bioinformatics tools for NGS data analyses.

• Journal of Pharmaceutical Investigation
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• v.34 no.1
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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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• v.20 no.1
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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.