• Genomics & Informatics
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• v.1 no.1
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• pp.1-6
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• 2003

In conclusion, the seemingly fuzzy and disorganized data of biology with thousands of different layers ranging from molecule to the Internet have refused so far to be mapped precisely and predicted successfully by mathematicians, physicists or computer scientists. Genomics and bioinformatics are the fields that process such complex data. The insights on the nature of biological entities as complex interaction networks are opening a door toward a generalization of the representation of biological entities. The main challenge of genomics and bioinformatics now lies in 1) how to data mine the networks of the domains of bioinformatics, namely, the literature, metabolic pathways, and proteome and structures, in terms of interaction; and 2) how to generalize the networks in order to integrate the information into computable genomic data for computers regardless of the levels of layer. Once bioinformatists succeed to find a general principle on the way components interact each other to form any organic interaction network at genomic scale, true simulation and prediction of life in silico will be possible.

• Journal of KIISE:Databases
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• v.30 no.6
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• pp.573-584
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• 2003

Recent massive data generation by genomics and proteomics requires bioinformatic tools to extract the biological meaning from the massive results. Here we introduce ROSPath, a database system to deal with information on reactive oxygen species (ROS)-mediated cell signaling pathways. It provides a structured repository for handling pathway related data and tools for querying, displaying, and analyzing pathways. ROSPath data model provides the extensibility for representing incomplete knowledge and the accessibility for linking the existing biochemical databases via the Internet. For flexibility and efficient retrieval, hierarchically structured data model is defined by using the object-oriented model. There are two major data types in ROSPath data model: ‘bio entity’ and ‘interaction’. Bio entity represents a single biochemical entity: a protein or protein state involved in ROS cell-signaling pathways. Interaction, characterized by a list of inputs and outputs, describes various types of relationship among bio entities. Typical interactions are protein state transitions, chemical reactions, and protein-protein interactions. A complex network can be constructed from ROSPath data model and thus provides a foundation for describing and analyzing various biochemical processes.

• Journal of the Korea Institute of Military Science and Technology
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• v.18 no.5
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• pp.582-593
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• 2015

For military training and course-of-action analysis, OneSAF Int'l version being used in ROK Army has a limited capability to simulate NBC(nuclear, biological, and chemical) damages. For high-fidelity NBC combat simulation, it is required to visualize NBC contamination dispersion in consideration of weather conditions and terrain characteristics. However, OneSAF itself handling interaction among thousands of combat entities cannot carry out a simulation of NBC contamination dispersion because it brings about an excess burden. To resolve this problem, this research aims to design simulation federation for analysis on NBC operational effects. After examining design consideration to connect OneSAF and a NBC contamination dispersion model, we design a federation architecture that facilitates the interaction between OneSAF and a NBC contamination dispersion model. Afterwards, we implement a federation interface to share simulation data by publish-subscribe pattern and to translate them into the proprietary format for each model. We prove the possibility of federation between both models, as showing that dispersion of NBC contaminated cloud and changes in concentration are reflected in OneSAF-based engagement simulation.