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

• Genomics & Informatics
• /
• v.8 no.2
• /
• pp.94-96
• /
• 2010

Integrating various pathway data collections to create new biological knowledge is a challenge, for which novel computational tools play a key role. For this purpose, we developed the Java-based conversion modules KGML2SBML and KGML2BioPAX to translate KGML (KEGG Markup Language) into a couple of common data exchange formats: SBML (Systems Biology Markup Language) and BioPAX (Biological Pathway Exchange). We hope that our work will be beneficial for other Java developers when they extend their bioinformatics system into SBML- or BioPAX-aware analysis tools. This is part of our ongoing effort to develop an ultimate KEGG-based pathway enrichment analysis system.

• Genomics & Informatics
• /
• v.5 no.2
• /
• pp.88-91
• /
• 2007

Repetitive sequences such as SINE, LINE, and LTR elements form a major part of eukaryotic genomes. A literature search tool that summarizes the information contained within repeat elements would provide biologists in the field of genomics with a useful tool for analyzing genomic sequence features. We developed a java program designed to make literature access easier by using two search engines simultaneously. RepWeb is a web-based search system that provides a user friendly interface for searching the reference data and journals for information related to repeat elements by using the search engines, Google Scholar and PubMed, simultaneously. It provides an interface that displays the repeat element- related biological information, and includes useful functions such as the production of a repeat tree, clickable links to PubMed and Google Scholar, exporting, and sorting a field into date, author, journal and title.

• Journal of the Korea Academia-Industrial cooperation Society
• /
• v.10 no.6
• /
• pp.1399-1406
• /
• 2009

Proteins are one of essential part of organisms; many proteins are enzymes that catalyze biochemical reactions and are vital to metabolism. Researching for 3D structure of proteins is important because functions of proteins are determined by 3D structure of them. In this study, we developed graphic tool that supports comparison and observation of the two proteins' 3D structure in the single screen. It also supports some comparison data to help researcher's easy comparison and observation works.

• Genomics & Informatics
• /
• v.5 no.4
• /
• pp.188-193
• /
• 2007

The Functional Element SNPs Database (FESD) categorizes functional elements in human genic regions and provides a set of single nucleotide polymorphisms (SNPs) located within each area. Users may select a set of SNPs in specific functional elements with haplotype information and obtain flanking sequences for genotyping. Our previous version of FESD has been improved in several ways. We regenerated all the data in FESD II from recently updated source data such as HapMap, UCSC GoldenPath, dbSNP, OMIM, and $TRANSFAC^{(R)}$. Users can obtain information about tagSNPs and simulate LD blocks for each gene from four ethnicities in the HapMap project on the fly. FESD II employs a Java/JSP web interface for better platform portability and higher speed than PHP in the previous version. As a result, FESD II provides its users with more powerful information about functional element SNPs of human ethnicities.

• Journal of Wetlands Research
• /
• v.15 no.1
• /
• pp.139-147
• /
• 2013

This study is thing about eco-tourism activated Mt. Gede Pangrango National Park in Indonesia. Indonesia is full of eco-tourist resources with the possession of the tropical forest. Particularly, Gede Pangrango National Park on the west of Java island has so plenty of bio-diversity that the UNESCO designated this park as the World Biosphere Reserve. By virtue of this, various visitors all over the world are visiting Gede Pangrango Park for doing research, education, hiking and camping. However, Indonesia lags behind other countries in convenience facilities for visitors, so their visiting programs are actually insufficient. In order for eco-tourism to be revitalized, there should be physical improvement in visiting facilities, management of a variety of visit programs, and local residents' participation & projects to increase the income of local residents. This study is going to seek for the environment-friendly management plan suited for the properties of the park and improvement plan for eco-visiting facilities by closely grasping the actual condition of the eco-tourism of Gede Pangrango National Park.

• Journal of Bio-Environment Control
• /
• v.13 no.4
• /
• pp.209-216
• /
• 2004

This study was aimed to assess the effects of microclimate factors on lettuce chlorophyll fluorescent responses and to develop an environment control system for plant growth by adopting a simple genetic algorithm. The photosynthetic responses measurements were repeated by changing one factor among six climatic factors at a time. The maximum Fv'/Fm' resulted when the ambient temperature was $21^{\circ}C,\;CO_2$ concentration range of 1,200 to 1,400 ppm, relative humidity of $68\%$, air current speed of $1.4m{\cdot}s^{-1}$, and the temperature of nutrient solution of $20^{\circ}C$. In PPF greater than $140{\mu}mol{\cdot}m^{-2}{\cdot}s^{-1}$, Fv'/Fm' values were decreased. To estimate the effects of combined microclimate factors on plant growth, a photosynthesis efficiency model was developed using principle component analysis for six microclimate factors. Predicted Fv'/Fm' values showed a good agreement to measured ones with an average error of $2.5\%$. In this study, a simple genetic algorithm was applied to the photosynthesis efficiency model for optimal environmental condition for lettuce growth. Air emperature of $22^{\circ}C$, root zone temperature of $19^{\circ}C,\;CO_2$ concentration of 1,400 ppm, air current speed of $1.0m{\cdot}s^{-1}$, PPF of $430{\mu}mol{\cdot}m^{-2}{\cdot}s^{-1}$, and relative humidity of $65\%$ were obtained. It is feasible to control plant environment optimally in response to microclimate changes by using photosynthesis efficiency model combined with genetic algorithm.

• Journal of Internet Computing and Services
• /
• v.16 no.1
• /
• pp.47-55
• /
• 2015

Recently, the environment of a hospital information system is a trend to combine various SMART technologies. Accordingly, various smart devices, such as a smart phone, Tablet PC is utilized in the medical information system. Also, these environments consist of various applications executing on heterogeneous sensors, devices, systems and networks. In these hospital information system environment, applying a security service by traditional access control method cause a problems. Most of the existing security system uses the access control list structure. It is only permitted access defined by an access control matrix such as client name, service object method name. The major problem with the static approach cannot quickly adapt to changed situations. Hence, we needs to new security mechanisms which provides more flexible and can be easily adapted to various environments with very different security requirements. In addition, for addressing the changing of service medical treatment of the patient, the researching is needed. In this paper, we suggest a dynamic approach to medical information systems in smart mobile environments. We focus on how to access medical information systems according to dynamic access control methods based on the existence of the hospital's information system environments. The physical environments consist of a mobile x-ray imaging devices, dedicated mobile/general smart devices, PACS, EMR server and authorization server. The software environment was developed based on the .Net Framework for synchronization and monitoring services based on mobile X-ray imaging equipment Windows7 OS. And dedicated a smart device application, we implemented a dynamic access services through JSP and Java SDK is based on the Android OS. PACS and mobile X-ray image devices in hospital, medical information between the dedicated smart devices are based on the DICOM medical image standard information. In addition, EMR information is based on H7. In order to providing dynamic access control service, we classify the context of the patients according to conditions of bio-information such as oxygen saturation, heart rate, BP and body temperature etc. It shows event trace diagrams which divided into two parts like general situation, emergency situation. And, we designed the dynamic approach of the medical care information by authentication method. The authentication Information are contained ID/PWD, the roles, position and working hours, emergency certification codes for emergency patients. General situations of dynamic access control method may have access to medical information by the value of the authentication information. In the case of an emergency, was to have access to medical information by an emergency code, without the authentication information. And, we constructed the medical information integration database scheme that is consist medical information, patient, medical staff and medical image information according to medical information standards.y Finally, we show the usefulness of the dynamic access application service based on the smart devices for execution results of the proposed system according to patient contexts such as general and emergency situation. Especially, the proposed systems are providing effective medical information services with smart devices in emergency situation by dynamic access control methods. As results, we expect the proposed systems to be useful for u-hospital information systems and services.