• International Journal of Contents
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• v.5 no.2
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• pp.6-15
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• 2009

Recently many different programming languages have emerged for the development of bioinformatics applications. In addition to the traditional languages, languages from open source projects such as BioPerl, BioPython, and BioJava have become popular because they provide special tools for biological data processing and are easy to use. However, it is not well-studied which of these programming languages will be most suitable for a given bioinformatics task and which factors should be considered in choosing a language for a project. Like many other application projects, bioinformatics projects also require various types of tasks. Accordingly, it will be a challenge to characterize all the aspects of a project in order to choose a language. However, most projects require some common and primitive tasks such as file I/O, text processing, and basic computation for counting, translation, statistics, etc. This paper presents the benchmarking results of six popular languages, Perl, BioPerl, Python, BioPython, Java, and BioJava, for several common and simple bioinformatics tasks. The experimental results of each language are compared through quantitative evaluation metrics such as execution time, memory usage, and size of the source code. Other qualitative factors, including writeability, readability, portability, scalability, and maintainability, that affect the success of a project are also discussed. The results of this research can be useful for developers in choosing an appropriate language for the development of bioinformatics applications.

• Proceedings of the Korean Information Science Society Conference
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• 2004.10b
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• pp.262-264
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• 2004

OMIM이나 MedLine과 같은 바이오 정보를 포함한 대규모의 데이터베이스에서의 바이오 정보검색이나 추출은 단계별 처리가 상호적인 운용에 의한 것이 아니라 수동 또는 Perl script에 의한 것이 대부분이다. 바이오정보(bio-information)의 효과적 추출과 유추를 위해서는 현재 상이한 스키마로 이루어진 다양한 데이터베이스들 간의 이질적 데이터(heterogeneous data)를 체계적이고 효율적으로 통합하는 표준 방안이 필요하다. 이를 위해서는 서로 다르게 표현된 다양한 개념간의 관계를 표현하는 지식체계가 필요하다. 본 연구에서는 이러한 지식체계인 온톨로지(ontology)와 자원 메타정보(metadata)를 표현하기 위한 국제적 표준안으로 대두되고 있는 시맨틱 웹(semantic web)에서 제공하는 온톨로지, 메타정보, 스키마 통합 안을 발전적으로 적용하여 이질적 바이오 정보의 효율적 통합처리 방안을 제시하고자 하였다.

• Bioinformatics and Biosystems
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• v.1 no.2
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• pp.99-102
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• 2006

The Basic Local Alignment Search Tool (BLAST) is one of the most established software in bioinformatics research and it compares a query sequence against the libraries of known sequences in order to investigate sequence similarity. Expressed Sequence Tags (ESTs) are single-pass sequence reads from mRNA (or cDNA) and represent the expression for a given cDNA library and the snapshot of genes expressed in a given tissue and/or at a given developmental stage. Therefore, ESTs can be very valuable information for functional genomics and bioinformatics researches. Although major bio database (DB) websites including NCBI are providing BLAST services and EST data, local DB and search system is demanding for better performance and security issue. Here we present animal EST DBs and local BLAST search system. The animal ESTs DB in NCBI Genbank were divided by animal species using the Perl script we developed. and we also built the new extended DB search systems fur the new data (Local Animal BLAST Search System: http://bioinfo.kohost.net), which was constructed on the high-capacity PC Cluster system fur the best performance. The new local DB contains 650,046 sequences for Bos taurus(cattle), 368,120 sequences for Sus scrofa (pig), 693,005 sequences for Gallus gallus (fowl), respectively.

• Journal of Physiology & Pathology in Korean Medicine
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• v.26 no.4
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• pp.551-556
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• 2012

The database for the oriental medicine had been existed in documentation in past times and it has been developed to the database type for random accesses in the information society. However, the aspects of the database are not so diversified and the database for the bio herbal material exists in widened type dictionary style. It is a situation that the database which handles the in-depth raw herbal medicines is not sufficient in its quantity and quality. Korean wild grape is a deciduous plant categorized into the Vitaceae and it was found experimentally that it has various medical effects. It is one of the medical materials with higher potentiality of academic study and commercialization recently because it has a bigger possibility to be applied into diverse industrial fields including the medical product for health, food and beauty. We constituted the cooperative system among the Muju cluster business group for Korean mountain wild grapes, Physiology Laboratory in Kyung Hee University Oriental Medicine and Medical Classics Laboratory in Kyung Hee University Oriental Medicine with a view to focusing on such potentiality and a database for Korean wild grapes was made a touchstone for establishing the in-depth database for the single bio medical materials. First of all, the literatures based on the North East Asia in ancient times had been categorized into the classical literature (Korean literature published by government organization, Korean classical literature, Chinese classical literature and classical literature fro Korean and Chinese oriental medicine) and modern literature (Modern literature for oriental medicine, modern literature for domestic and foreign herbal medicine) to cover the eastern and western research records and writings related to Korean wild grapes and the text-mining work has been performed through the cooperation system with the Medical Classics Laboratory in Kyung Hee University Oriental Medicine. First of all, the data for the experiment and theory for Korean wild grape were collected for the Medline database controlled by the Parliament Library of USA to arrange the domestic and foreign theses with topic for Korean wild grapes and the network hyperlink function and down load function were mounted for self-thesis searching function and active view based on the collected data. The thesis searching function provides various auxiliary functions and the searching is available according to the diverse searching/queries such as the name of sub species of Korean wild grape, the logical intersection index for the active ingredients, efficacy and elements. It was constituted for the researchers who design the Korean wild grape study to design of easier experiment. In addition, the data related to the patents for Korean wild grape which were collected from European Patent Office in response to the commercialization possibility and the system available for searching and view was established in the same viewpoint. Perl was used for the query programming and MS-SQL for database establishment and management in the designing of this database. Currently, the data is available for free use and the address is as follows. http://163.180.41.43:8011/index.html