• Genomics & Informatics
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• v.15 no.1
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• pp.11-18
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• 2017

Nowadays, huge volumes of chromatin immunoprecipitation-sequencing (ChIP-Seq) data are generated to increase the knowledge on DNA-protein interactions in the cell, and accordingly, many tools have been developed for ChIP-Seq analysis. Here, we provide an example of a streamlined workflow for ChIP-Seq data analysis composed of only four packages in Bioconductor: dada2, QuasR, mosaics, and ChIPseeker. 'dada2' performs trimming of the high-throughput sequencing data. 'QuasR' and 'mosaics' perform quality control and mapping of the input reads to the reference genome and peak calling, respectively. Finally, 'ChIPseeker' performs annotation and visualization of the called peaks. This workflow runs well independently of operating systems (e.g., Windows, Mac, or Linux) and processes the input fastq files into various results in one run. R code is available at github: https://github.com/ddhb/Workflow_of_Chipseq.git.

• Korean Journal of Computational Design and Engineering
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• v.20 no.4
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• pp.431-442
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• 2015

Currently, a BIM-based quantity takeoff (QTO) system is mainly focused on architectural projects. To perform this, diverse quantity takeoff methods such as an object-based automatic quantity takeoff, manual quantity and base functions of calculation have widely been utilizing. However, since BIM library for road projects includes structural elements associated with alignment, it is necessary to establish cost estimation system interlocked with historical cost using 3D library by each unit length. Accordingly, the aim of this study is to develop cost estimation model with using a historical cost approach so that it can be utilized in construction planning based on the BIM library for road projects. For this, based on the BIM library for road, the standardized quantity is estimated, and a process for calculating historical cost and a verification model with a 5D simulation was developed by mapping a WBS code with each BIM library object. This can be applied during the approximate cost estimation process in a project planning and an initial design phase for road projects. Besides, it is expected that these results will be utilized in constructing an optimal historical cost estimation process for project libraries.

• Journal of the Korean Society for Aeronautical & Space Sciences
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• v.43 no.9
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• pp.805-813
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• 2015

This paper introduces the development of temperature mapping code between thermal mesh and structural mesh in KARI Satellite Design Software. Generally, temperature distribution of a satellite varies with the time by the space environment of the orbit, so thermal expansion of the structure should be analysed in design of the satellite. For the sake of the coupled thermal structural analysis, an interpolation algorithm between two finite element heterogeneous grids has been proposed by which temperature transfer is successively conducted.

• Journal of Radiation Protection and Research
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• v.37 no.3
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• pp.146-148
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• 2012

The use of GEANT4 simulation toolkit has increased in the radiation medical field for the design of treatment system and the calibration or validation of treatment plans. Moreover, it is used especially on calculating dose simulation using medical data for radiation therapy. However, using internal visualization tool of GEANT4 detector constructions on expressing dose result has deficiencies because it cannot display isodose line. No one has attempted to use this code to a real patient's data. Therefore, to complement this problem, using the result of gMocren that is a three-dimensional volume-visualizing tool, we tried to display a simulated dose distribution and isodose line on medical image. In addition, we have compared cross-validation on the result of gMocren and GEANT4 simulation with commercial radiation treatment planning system. We have extracted the analyzed data of dose distribution, using real patient's medical image data with a program based on Monte Carlo simulation and visualization tool for radiation isodose mapping.

• KIPS Transactions on Computer and Communication Systems
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• v.4 no.5
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• pp.153-160
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• 2015

The effectiveness of multicores depends on how well a scheduler can assign tasks onto the cores efficiently. In a heterogeneous multicore platform, the execution time of an application depends on which core it executes on. That is to say, the effectiveness of task assignment is one of the important components for a multicore systems' performance. This work proposes a load scheduling technique that analyzes execution time of each task by profiling. The profiling result provides a basic information to predict which task-to-core mapping is likely to provide the best performance. By using such information, the proposed technique is about 26% performance gain.

• The Transactions of the Korea Information Processing Society
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• v.4 no.10
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• pp.2434-2444
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• 1997

As software industry progresses, the necessity of visual information have increased more than text-oriented information. So, automatic tools are required to satisfy a user's desire for visual design representation of various source information in the real-world. In this paper, we discuss the methodology and tools for parsing abstract information through semantic analysis and extracting visual information through visual mapping. Namely, as to abstract informations are represented as relational structure and then mapped into visual structure using regular rule, user can obtain visual information. We suggest VOLS(Visual Object Layout System) to transform a abstract information to visual information. It can improve user understandability and assist a maintenance for existing source code.

• Journal of KIISE:Computing Practices and Letters
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• v.12 no.1
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• pp.43-55
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• 2006

In this paper, we present a framework which is used to develop, modify, maintain and extend a control and monitoring software easily for any kind of automatic instruments. The proposed framework is composed of three XML documents (IID, MAP, CMIML) and two tools (Virtual Instrument Wizard, Generator). Interface information of behaviors and states of instrument is written on IID. Mapping information between the interface information in IID and API of a real instrument driver is written on MAP Final information of the control and monitoring software is written on CMIML, IID, MAP and CMIML are written by XML format to provide a common usage and platform independence of the proposed framework. Vl Wizard generates CMIML intermediate platform independent document using IID and existing CMIML, and Generator generates the source code of a control and monitoring software platform dependent code automatically using CMIML and MAP. The suggested framework provides an easy development and maintenance because it automatically generates a control and monitoring software in GUI environment and it also provides common usage and platform independence in virtue of using description document of XML format. Also, reusability can be increased by reusing platform independent software description document and not reusing platform dependent software code.

• Journal of KIISE
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• v.44 no.1
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• pp.1-12
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• 2017

The continuously growing internet service requirements has resulted in a multitier system structure consisting of web server and database (DB) server. In this multitier structure, the existing intrusion detection system (IDS) detects known attacks by matching misused traffic patterns or signatures. However, malicious change to the contents at DB server through hypertext transfer protocol (HTTP) requests at the DB server cannot be detected by the IDS at the DB server's end, since the DB server processes structured query language (SQL) without knowing the associated HTTP, while the web server cannot identify the response associated with the attacker's SQL query. To detect these types of attacks, the malicious user is tracked using knowledge on interaction between HTTP request and SQL query. However, this is a practical challenge because system's source code analysis and its application logic needs to be understood completely. In this study, we proposed a scheme to find the HTTP request associated with a given SQL query using only system log files. We first generated an HTTP request-SQL query map from system log files alone. Subsequently, the HTTP request associated with a given SQL query was identified among a set of HTTP requests using this map. Computer simulations indicated that the proposed scheme finds the HTTP request associated with a given SQL query with 94% accuracy.

• Journal of KIISE:Computing Practices and Letters
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• v.8 no.2
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• pp.174-182
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• 2002

The object-oriented design methods and their CASE tools are widely used in practice by many real-time software developers. However, object-oriented CASE tools require an additional step of identifying tasks from a given design model. Unfortunately, it is difficult to automate this step for a couple of reasons: (1) there are inherent discrepancies between objects and tasks; and (2) it is hard to derive tasks while maximizing real-time schedulability since this problem makes a non-trivial optimization problem. As a result, in practical object-oriented CASE tools, task identification is usually performed in an ad-hoc manner using hints provided by human designers. In this paper, we present a systematic, schedulability-aware approach that can help mapping real-time object-oriented models to multi-threaded implementations. In our approach, a task contains a group of mutually exclusive transactions that may possess different periods and deadline. For this new task model, we provide a new schedulability analysis algorithm. We also show how the run-time system is implemented and how executable code is generated in our frame work. We have performed a case study. It shows the difficulty of task derivation problem and the utility of the automated synthesis of implementations as well as the Inappropriateness of the single-threaded implementations.

• Journal of the Computational Structural Engineering Institute of Korea
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• v.32 no.6
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• pp.349-357
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• 2019

Finite element method (FEM) is utilized in the development of products to realistically analyze and predict the mechanical behavior of materials in various fields. However, the approach based on the numerical analysis of glass fiber reinforced plastic (GFRP) composites, for which the fiber orientation and strain rate affect the mechanical properties, has proven to be challenging. The purpose of this study is to define and evaluate the mechanical properties of glass fiber reinforced plastic composites using the numerical analysis models of Digimat, a linear, nonlinear multi-scale modeling program for various composite materials such as polymers, rubber, metal, etc. In addition, the aim is to predict the behavior of realistic polymeric composites. In this regard, the tensile properties according to the fiber orientation and strain rate of polybutylene terephthalate (PBT) with short fiber weight fractions of 30wt% among various polymers were investigated using references. Information on the fiber orientation was calculated based on injection analysis using Moldflow software, and was utilized in the finite element model for tensile specimens via a mapping process. LS-Dyna, an explicit commercial finite element code, was used for coupled analysis using Digimat to study the tensile properties of composites according to the fiber orientation and strain rate of glass fibers. In addition, the drawbacks and advantages of LS-DYNA's various anisotropic material models were compared and evaluated for the analysis of glass fiber reinforced plastic composites.