2.BioSubroutine: an Open Web Server for Bioinformatics Algorithms and Subroutines.
Joowon LEE ; Hana KIM ; Wonhye LEE ; Dongil CHUNG ; Jong BHAK
Genomics & Informatics 2005;3(1):35-38
We present BioSubroutine, an open depository server that automatically categorizes various subroutines frequently used in bioinformatics research. We processed a large bioinformatics subroutine library called Bio.pl that was the first Bioperl subroutine library built in 1995. Over 1000 subroutines were processed automatically and an HTML interface has been created. BioSubroutine can accept new subroutines and algorithms from any such subroutine library, as well as provide interactive user forms. The subroutines are stored in an SQL database for quick searching and accessing. BioSubroutine is an open access project under the BioLicense license scheme.
Computational Biology*
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Licensure
3.COCAW: A Genome-wide Pattern Search System for Designing Microbial Probes.
Seunghee RYU ; Kiejung PARK ; Dohoon LEE ; Cheol Min KIM
Genomics & Informatics 2009;7(3):178-180
A few bioinformatics tools have been used to find out conserved regions as probes. We have developed a system based on a heuristic method with web interfaces to find out conserved regions against microbial genomes. The system runs in real time by using relative entropy in limited narrow regions and detecting similar regions between pair regions with local alignment. The system could be useful to find out conserved regions as genome-wide scale.
Computational Biology
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Entropy
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Genome
4.The AB05 NIAB Tools Workbench for Building Automatic Biopathway Maps for Agricultural Organisms.
Mi Kyung CHO ; Kyung Oh YOON ; Hyun Seok PARK
Genomics & Informatics 2007;5(4):200-202
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.
Agriculture
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Computational Biology
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Licensure
6.Parsing KEGG XML Files to Find Shared and Duplicate Compounds Contained in Metabolic Pathway Maps: A Graph-Theoretical Perspective.
Sung Hui KANG ; Myung Ha JANG ; Jiyoung WHANG ; Hyun Seok PARK
Genomics & Informatics 2008;6(3):147-152
The basic graph layout technique, one of many visualization techniques, deals with the problem of positioning vertices in a way to maximize some measure of desirability in a graph. The technique is becoming critically important for further development of the field of systems biology. However, applying the appropriate automatic graph layout techniques to the genomic scale flow of metabolism requires an understanding of the characteristics and patterns of duplicate and shared vertices, which is crucial for bioinformatics software developers. In this paper, we provide the results of parsing KEGG XML files from a graph-theoretical perspective, for future research in the area of automatic layout techniques in biological pathway domains.
Computational Biology
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Metabolic Networks and Pathways
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Systems Biology
7.Design of an Integration System for Bioinformatics Data Sources Using a Global MDR.
Journal of Korean Society of Medical Informatics 2008;14(2):189-199
OBJECTIVES: Nowadays, as the amounts of biological data are rapidly increasing, bioinformatics has become one of the important research issues. The bioinformatics data sources are, however, distributed and heterogeneous, and therefore, often poorly integrated and difficult to use together. As many bioinformatics analyses need to make use of multiple information sources, the problem of integration of bioinformatics data sources has become an important one. The purpose of this paper is to present an integration system for bioinformatics data sources. METHODS: To solve this problem, we present an integration system for bioinformatics data sources using a global MDR, which provides users with efficiency and convenience as if they use one system. We deal with the extraction of data elements for bioinformatics MDRs by using ISO 11179 mandatory attributes. RESULTS: A global bioinformatics MDR schema for given MDRs and the results of query processing are presented. CONCLUSIONS: The proposed system and concepts in this paper may be a good solution for the integration of diverse bioinformatics data sources.
Computational Biology
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Information Storage and Retrieval
8.Bioinformatics Resources of the Korean Bioinformation Center (KOBIC).
Byungwook LEE ; In Sun CHU ; Namshin KIM ; Jinhyuk LEE ; Seon Yong KIM ; Wan Kyu KIM ; Sanghyuk LEE
Genomics & Informatics 2010;8(4):165-169
The Korean Bioinformation Center (KOBIC) is a national bioinformatics research center in Korea. We developed many bioinformatics algorithms and applications to facilitate the biological interpretation of OMICS data. Here we present an introduction to major bioinformatics resources of databases and tools developed at KOBIC. These resources are classified into three main fields: genome, proteome, and literature. In the genomic resources, we constructed several pipelines for next generation sequencing (NGS) data processing and developed analysis algorithms and web-based database servers including miRGator, ESTpass, and CleanEST. We also built integrated databases and servers for microarray expression data such as MDCDP. As for the proteome data, VnD database, WDAC, Localizome, and CHARMM_HM web servers are available for various purposes. We constructed IntoPub server and Patome database in the literature field. We continue constructing and maintaining the bioinformatics infrastructure and developing algorithms.
Computational Biology
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Genome
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Korea
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Proteome
9.Computational Challenges for Integrative Genomics.
Genomics & Informatics 2004;2(1):7-18
Integrated genomics refers to the use of large-scale, systematically collected data from various sources to address biological and biomedical problems. A critical ingredient to a successful research program in integrated genomics is the establishment of an effective computational infrastructure. In this review, we suggest that the computational infrastructure challenges include developing tools for heterogeneous data organization and access, innovating techniques for combining the results of different analyses, and establishing a theoretical framework for integrating biological and quantitative models. For each of the three areas - data integration, analyses integration, and model integration - we review some of the current progress and suggest new topics of research. We argue that the primary computational challenges lie in developing sound theoretical foundations for understanding the genome rather than simply the development of algorithms and programs.
Computational Biology
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Foundations
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Genome
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Genomics*
10.IdMapper: A Java Application for ID Mapping across Multiple Cross-referencing Providers.
Hookeun LEE ; Hyeonjin KIM ; Ungsik YU
Genomics & Informatics 2009;7(4):208-211
We developed an identifier mapping application for bioinformatics research in Java programming language. It is easy to use and provides many usability functionalities that are expected as essentials for a professional application. It supports three widely used mapping services and can convert many ids from one source database into many target databases at once. Id mapping across service providers is possible by remapping the resultant ids. Because it adheres to the NetBeans platform architecture, it can be incorporated into other NetBeans platform applications as an id mapping provider without adaption or modification.
Computational Biology
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Indonesia
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Programming Languages