• Genomics & Informatics
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• v.3 no.3
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• pp.94-97
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• 2005

We have built a database server called Patome which contains the annotation information for patented bio-sequences from the Korean Intellectual Property Office (KIPO). The aims of the Patome are to annotate Korean patent bio-sequences and to provide information on patent relationship of public database entries. The patent sequences were annotated with Reference Sequence (RefSeq) or NCBI's nr database. The raw patent data and the annotated data were stored in the database. Annotation information can be used to determine whether a particular RefSeq ID or NCBI's nr ID is related to Korean patent. Patome infrastructure consists of three components­the database itself, a sequence data loader, and an online database query interface. The database can be queried using submission number, organism, title, applicant name, or accession number. Patome can be accessed at http://www.patome.net. The information will be updated every two months.

• Genomics & Informatics
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• v.7 no.3
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• pp.175-177
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• 2009

We have developed WinBioDBs with Windows interfaces, which include importing modules and searching interfaces for 10 major public databases such as GenBank, PIR, SwissProt, Pathway, EPD, ENZYME, REBASE, Prosite, Blocks, and Pfam. User databases can be constructed with searching results of queries and their entries can be edited. The program is a stand-alone database searching program on Windows PC. Database update features are supported by importing raw database files and indexing after downloading them. Users can adjust their own searching environments and report format and construct their own projects consisting of a combination of a local databases. WinBioDBs are implemented with VC++ and its database is based on MySQL.

• Proceedings of the KSRS Conference
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• 2005.10a
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• pp.280-282
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• 2005

A ribonucleic acid (RNA) is one of the two types of nucleic acids found in living organisms. An RNA molecule represents a long chain of monomers called nucleotides. The sequence of nucleotides of an RNA molecule constitutes its primary structure, and the pattern of pairing between nucleotides determines the secondary structure of an RNA. Non-coding RNA genes produce transcripts that exert their function without ever producing proteins. Predicting the secondary structure of non-coding RNAs is very important for understanding their functions. We focus on Nussinov's algorithm as useful techniques for predicting RNA secondary structures. We introduce a new traceback matrix and scoring table to improve above algorithm. And the improved algorithm provides better levels of performance than the originals.

• Genomics & Informatics
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• v.3 no.1
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• pp.35-38
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• 2005

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.

• Proceedings of the Korea Contents Association Conference
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• 2009.05a
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• pp.1180-1185
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• 2009

Database is constructed according to the development of information contents technology. But the construction of database using bio-information has not been developed. because it is difficult to collect bio-information. This paper presents how to construct database about sensing temperature and tilt of cow based on bio-information using RF communication. The system consists of 8bit micro-controller, tilt sensor, temperature sensor and RF module.

• Proceedings of the Korea Contents Association Conference
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• 2003.11a
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• pp.285-289
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• 2003

In this paper, we present DTD-dependent object database schema design methods to efficiently store XML data and process path expression. The similarity between DTD graph model and the object database model, and the characteristics of object database, object references and set-valued attributes, are very profitable to store XML documents into object databases. We propose two kinds of schema design methods. We then compare and anayze space and time complexity for the methods.

• Proceedings of the Korea Information Processing Society Conference
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• 2005.11a
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• pp.15-18
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• 2005

A ribonucleic acid (RNA) is one of the two types of nucleic acids found in living organisms. An RNA molecule represents a long chain of monomers called nucleotides. The sequence of nucleotides of an RNA molecule constitutes its primary structure, and the pattern of pairing between nucleotides determines the secondary structure of an RNA. Non-coding RNA genes produce transcripts that exert their function without ever producing proteins. Predicting the secondary structure of non-coding RNAs is very important for understanding their functions. We focus on Nussinov's algorithm as useful techniques for predicting RNA secondary structures. We introduce a new traceback matrix and scoring table to improve above algorithm. And the improved prediction algorithm provides better levels of performance than the originals.

• Genomics & Informatics
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• v.6 no.2
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• pp.95-97
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• 2008

Many bioinformatics sites have managed local bio-databases, including major databases such as GenBank and PIR with update load. We have developed several programs to monitor the update status of these databases and to FTP them automatically. These programs can be used for maintaining local bio-databases as recent versions and providing up-to-date databases through FTP sites. Currently, the program serves major bio-databases and will extend to accommodate many more bio-databases.

• Journal of Animal Environmental Science
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• v.21 no.1
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• pp.9-20
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• 2015

The livestock manure recycling have been performed worldwide because of its environmental and economic benefits. However, domestic standard protocol was nothing for high solid manure. Therefore, This paper was conducted to review database configuration of manure characteristics, analysis methods, bio-methane potential test for high solid manure recycling. In American society of agricultural engineers standard, manure characteristics indicated about sort of thirty types. This is important information to determine for manure recycling method. Furthermore, in order to determine exact manure characteristics recommended that synchronized chemical analysis method among studies. Bio-methane potential tests are widely performed in studies about estimation of organic substrates methane production. Although various methods and parameters were used, was no standard protocol and guideline in domestic. Bio-methane potential test methods and parameters were reviewed through various researches. Consequently, this paper is expected that assist to additional studies and manure characteristic database.

• Proceedings of the Korean Institute of Intelligent Systems Conference
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• 2003.09a
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• pp.11-15
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• 2003

Amount of biological data information has been increasing exponentially. In order to cope with this bio-information explosion, it is necessary to construct a biological data information integration system. The integration system could provide useful services for bio-application developers by answering general complex queries that require accessing information from heterogeneous bio data sources, and easily accommodate a new database into the integrated systems. In this paper, we analyze architectures and mechanisms of existing integration systems with their advantages and disadvantages. Based on this analysis and user requirement studies, we propose an integration system framework that embraces advantages of the existing systems. More specifically, we propose an integration system architecture composed of a mediator and wrappers, which can offer a service interface layer for various other applications as well as independent biologists, thus playing the role of database management system for biology applications. In other words, the system can help abstract the heterogeneous information structures and formats from the application layer. In the system, the wrappers send database-specific queries and report the result to the mediator using XML. The proposed system could facilitate in silico knowledge discovery by allowing combination of numerous discrete biological information databases.