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Analysis of a Large-scale Protein Structural Interactome: Ageing Protein structures and the most important protein domain

  • Bolser, Dan;Dafas, Panos;Harrington, Richard;Schroeder, Michael;Park, Jong
    • 한국생물정보학회:학술대회논문집
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    • 한국생물정보시스템생물학회 2003년도 제2차 연례학술대회 발표논문집
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    • pp.26-51
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    • 2003
  • Large scale protein interaction maps provide a new, global perspective with which to analyse protein function. PSIMAP, the Protein Structural Interactome Map, is a database of all the structurally observed interactions between superfamilies of protein domains with known three-dimensional structure in thePDB. PSIMAP incorporates both functional and evolutionary information into a single network. It makes it possible to age protein domains in terms of taxonomic diversity, interaction and function. One consequence of it is to predict the most important protein domain structure in evolution. We present a global analysis of PSIMAP using several distinct network measures relating to centrality, interactivity, fault-tolerance, and taxonomic diversity. We found the following results: ${\bullet}$ Centrality: we show that the center and barycenter of PSIMAP do not coincide, and that the superfamilies forming the barycenter relate to very general functions, while those constituting the center relate to enzymatic activity. ${\bullet}$ Interactivity: we identify the P-loop and immunoglobulin superfamilies as the most highly interactive. We successfully use connectivity and cluster index, which characterise the connectivity of a superfamily's neighbourhood, to discover superfamilies of complex I and II. This is particularly significant as the structure of complex I is not yet solved. ${\bullet}$ Taxonomic diversity: we found that highly interactive superfamilies are in general taxonomically very diverse and are thus amongst the oldest. This led to the prediction of the oldest and most important protein domain in evolution of lift. ${\bullet}$ Fault-tolerance: we found that the network is very robust as for the majority of superfamilies removal from the network will not break up the network. Overall, we can single out the P-loop containing nucleotide triphosphate hydrolases superfamily as it is the most highly connected and has the highest taxonomic diversity. In addition, this superfamily has the highest interaction rank, is the barycenter of the network (it has the shortest average path to every other superfamily in the network), and is an articulation vertex, whose removal will disconnect the network. More generally, we conclude that the graph-theoretic and taxonomic analysis of PSIMAP is an important step towards the understanding of protein function and could be an important tool for tracing the evolution of life at the molecular level.

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영상장치의 표현특성이 공간에 미치는 영향 (Effects of the Space in Image Equipment Characteristic)

  • 유재엽
    • 한국디자인학회:학술대회논문집
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    • 한국디자인학회 2004년도 춘계 학술발표대회 논문집
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    • pp.44-45
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    • 2004
  • 현대 산업사회에서 정보기기의 발달은 영상이 멀티미디어, 정보 전달 매체 도구, 예술 커뮤니케이션 도구로서 다양하게 표현되고 있다. 이러한 영상은 재현의 장치이며 소리와 빛 음이 복합적으로 형성된 시청각적 이미지 전달매체이다. 영상이 지니는 직관적이며 감각적인 표시성은 대상물을 재현하고 동시성을 지닌 커뮤니케이션 도구로서 또는 의미 전달체로서 허구, 사실, 비 허구, 비 사실을 모두 나타낼 수 가 있다. 바로 이러한 점 때문에 앞으로 영상의 영역은 점차 넓혀질 것이며 우리가 살고 있는 공간 속에서 감각되는 인식의 세계는 다양하게 흡수하여 반응하게 될 것이다. 이에 다양한 영역으로 확대되고 있는 영상장치와 이를 포함한 공간과의 관계설정 측면에서 본 연구는 영상과 공간이 내포하고 있을 환경적 의미 즉, 영상과 공간, 인간과 상호연관성에 대한 인식을 바탕으로 공간적 장치로서 공간 속에서 영상매체와 장치가 어떠한 영향을 미치는지 고찰하였다. 연구 결과로서 영상장치가 공간에 미치는 영향과 표현 특성은 '상호교감의 표현매체', '형이상학적 초 피막 공간 구성제','오브제'의 3가지 측면으로 제시하였다. 본 연구를 토대로 영상장치와 공간과의 관계 의미 분석을 통한 영상 설치물의 목적별 공간 접근 방법과 공간 레리아웃의 틀을 기대할 수 있다.

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수리 모형을 이용한 Korea Land Data Assimilation System (KLDAS) 자료의 수문자료에 대한 영향력 분석 (Interactions between Soil Moisture and Weather Prediction in Rainfall-Runoff Application : Korea Land Data Assimilation System(KLDAS))

  • 정용;최민하
    • 한국방재학회:학술대회논문집
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    • 한국방재학회 2011년도 정기 학술발표대회
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    • pp.172-172
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    • 2011
  • The interaction between land surface and atmosphere is essentially affected by hydrometeorological variables including soil moisture. Accurate estimation of soil moisture at spatial and temporal scales is crucial to better understand its roles to the weather systems. The KLDAS(Korea Land Data Assimilation System) is a regional, specifically Korea peninsula land surface information systems. As other prior land data assimilation systems, this can provide initial soil field information which can be used in atmospheric simulations. For this study, as an enabling high-resolution tool, weather research and forecasting(WRF-ARW) model is applied to produce precipitation data using GFS(Global Forecast System) with GFS embedded and KLDAS soil moisture information as initialization data. WRF-ARW generates precipitation data for a specific region using different parameters in physics options. The produced precipitation data will be employed for simulations of Hydrological Models such as HEC(Hydrologic Engineering Center) - HMS(Hydrologic Modeling System) as predefined input data for selected regional water responses. The purpose of this study is to show the impact of a hydrometeorological variable such as soil moisture in KLDAS on hydrological consequences in Korea peninsula. The study region, Chongmi River Basin, is located in the center of Korea Peninsular. This has 60.8Km river length and 17.01% slope. This region mostly consists of farming field however the chosen study area placed in mountainous area. The length of river basin perimeter is 185Km and the average width of river is 9.53 meter with 676 meter highest elevation in this region. We have four different observation locations : Sulsung, Taepyung, Samjook, and Sangkeug observatoriesn, This watershed is selected as a tentative research location and continuously studied for getting hydrological effects from land surface information. Simulations for a real regional storm case(June 17~ June 25, 2006) are executed. WRF-ARW for this case study used WSM6 as a micro physics, Kain-Fritcsch Scheme for cumulus scheme, and YSU scheme for planetary boundary layer. The results of WRF simulations generate excellent precipitation data in terms of peak precipitation and date, and the pattern of daily precipitation for four locations. For Sankeug observatory, WRF overestimated precipitation approximately 100 mm/day on July 17, 2006. Taepyung and Samjook display that WRF produced either with KLDAS or with GFS embedded initial soil moisture data higher precipitation amounts compared to observation. Results and discussions in detail on accuracy of prediction using formerly mentioned manners are going to be presented in 2011 Annual Conference of the Korean Society of Hazard Mitigation.

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Evaluation of the Accuracy of Distance Measurements on 3D Volume-rendered Image of Human Skull Using Multi-detector CT: Effects of Acquisition Section Thickness and Reconstruction Section Thickness

  • Haijo Jung;Kim, Hee-Joung;Lee, Sang-Ho;Kim, Dong-Wook;Soonil Hong;Kim, Dong-Hyeon;Son, Hye-Kyung;Wonsuk Kang;Kim, Kee-Deog
    • 한국의학물리학회:학술대회논문집
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    • 한국의학물리학회 2002년도 Proceedings
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    • pp.457-460
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    • 2002
  • The image quality of three-dimensional (3D) images has been widely investigated by the qualitative analysis method. A need remains for an objective and quantitative method to assess the image quality of 3D volume-rendered images. The purpose of this study was to evaluate the quantitative accuracy of distance measurements on 3D volume-rendered images of a dry human skull by using multi-detector computed tomography (MDCT). A radiologist measured five times the twenty-one direct measurement line items composed among twelve reference points on the skull surface with a digital vernier caliper. The water filled skull specimen was scanned with a MDCT according to the section thicknesses of 1.25, 2.50, 3.75, and 5.00 mm for helical (high quality; pitch 3:1) scan mode. MDCT data were reconstructed with its acquisition section thickness and with 1.25 mm section thickness for all scans. An observer also measured seven times the corresponding items on 3D volume-rendered images with measuring tools provided by volumetric analysis software. The quantitative accuracy of distance measurements on the 3D volume-rendered images was statistically evaluated (p-value < 0.05) by comparatively analyzing these measurements with the direct distance measurements. The accuracy of distance measurements on the 3D volume-rendered MDCT images acquired with 1.25, 2.50, 3,75 and 5.00 mm section thickness and reconstructed with its section thickness were 48%, 33%, 23%, and 14%, respectively. Meanwhile, there were insignificant statistical differences in accuracy of distance measurements among 3D volume-rendered images reconstructed with 1.25 mm section thickness for the each acquisition section thickness. MDCT images acquired with thick section thickness and reconstructed with thin section thickness in helical scan mode should be effectively used in medical planning of 3D volume-rendered images. The quantitative analysis of distance measurement may be a useful tool for evaluating the quantitative accuracy and the defining optimal parameters of 3D volume-rendered CT images.

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Virtual Dissection System of Cadaver Heart Using 3-Dimensional Image

  • Chung, Min-Suk;Lee, Je-Man;Kim, Min-Koo;Park, Seung-Kyu
    • 대한의용생체공학회:학술대회논문집
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    • 대한의용생체공학회 1997년도 추계학술대회
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    • pp.357-360
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    • 1997
  • For medical students and doctors, knowledge of the 3-dimensional (3D) structure of the heart is very important in diagnosis and treatment of the heart diseases. 2-dimensional (2D) tools (e.g. anatomy book) or classical 3D tools (e.g. plastic model) are not sufficient or understanding the complex structures of the heart. Moreover, it is not always guaranteed to dissect the heart of cadaver when it is necessary. To overcome this problem, virtual dissection systems of the heart have been developed. But these systems are not satisfactory since they are made of radiographs; they are not true 3D images; they can not be used to dissect freely; or they can only be operated on the workstation. It is also necessary to make the dissection systems incorporating the various races and tribes because of the organ's difference according to race and tribe. This study was intended to make the 3D image of the heart from a Korean cadaver, and to establish a virtual dissection system of the heart with a personal computer. The procedures or manufacturing this system were as follows. 1. The heart from a Korean adult cadaver was embedded with gelatin solution, and serially cross-sectioned at 1mm-thickness on a meat slicer. Pictures or 153 cross-sectioned specimens were inputted into the computer using a digital camera ($756{\times}504$ resolution, true color). 2. The alignment system was established by means of the language of IDL, and applied to align 2D images of the heart. In each of 2D images, closed curves lining clean and dirty blood pathways were drawn manually on the CorelDRAW program. 3. Using the language of IDL, the 3D image and the virtual dissection system of the heart were constructed. The virtual dissection system of the heart allowed or ree rotation, any-directional sectioning, and selected visualization of the heart's structure. This system is expected to become more advanced, and to be used widely through Internet or CD-title as an educational tool for medical students and doctors.

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6TALK : Implementation of NAT-PT/SIIT and enhanced ALG

  • 이주철;호용근;신명기;김형준
    • 한국정보통신학회:학술대회논문집
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    • 한국해양정보통신학회 2002년도 추계종합학술대회
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    • pp.701-705
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    • 2002
  • 본 논문에서는 6TALK (IPv6 TrAansLator of Krv6) 프로젝트의 구현에 대한 내용과, 이를 이용하여 IPv6 망이 기존의 IPv4망이나, 다른 IPv6망과 자연스럽게 연동할 수 있는 시나리오에 관해 기술한다. 이미 잘 알려진 바와 같이 현재의 IPv4 인터넷은 인터넷 사용자의 폭발적인 급증과 더불어 한계를 맞이하고 있다. 이를 극복하기 위해 제안된 IPv6는 현재 여러 기술적인 표준화와 실험 망에서의 테스트 과정을 마무리 짓고 있는 단계이다. 앞으로의 IPv6의 보급에 있어 가장 중요한 과정은 기존에 널리 존재하고 있는 IPv4망과 자연스럽게 공존하며 그 적용 범위를 넓혀갈 수 있도록 하는 전이 기술을 개발, 보급하는 일이다 이를 위해서 IETF에서는 NGTrans라는 WG을 별도로 만들어 IPv6로의 전환에 관련된 기술들을 표준화하고 있다. 현재 전 세계적으로 다양한 IPv6 관련 전환기술 프로젝트들이 진행되고 있으며, 본 논문에서 소개하는 6TALK 프로젝트도 NGTrans WG에서 소개하는 기술들을 바탕으로 망의 구성에 따라 IPv4망과 IPv6망이 자연스럽게 공존할 수 있도록 하는 솔루션들을 제공하는 것을 최종 목표로 하는 프로젝트이다. NGTrans WG에서 제안한 전환기술은 듀얼스택, 터널링, 변환기 등과 같은 기본 기술들과, 이 기본 기술을 확장 응용한 기술들로 이루어져 있다. 6TALK는 이러한 전환기술들을 복합적으로 사용하며, 네트워크의 가장자리(edge)에 존재하는 IPv6망이 기존 IPv4망이나, IPv4 망을 사이에 두고 존재하는 IPv6망과 연동할 수 있도록 하는 기능을 제공한다. 6TALK은 전이기술로 NAT-PT/SIIT와 몇몇 응용레벨 프로토콜에 대한 ALG, 구현환경으로는 커널 2.4.18버전이 탑재된 리눅스를 이용하고 있다.d it apply a electronic cash system. In particularly a proposed electronic cash system have an anonymity control ability which trace a user who make use a electronic cash illegally in association with a trusted center.estigation and explain how our tool can be further enhanced.door playground facilities. On the basis of the site investigation the interview and the indoor education program for physically challenged children the author completed an outside play program. Each item in this program was classified as belonging to either a "sense play" program or and "exercise play" program. Finally, the author designed suitable play equipment for physically challenged children corresponding to each item in the exercise programs in order to research the appropriateness of the equipment to its intended use. This research is the first step. From this point the author expects that sp

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Targeting Analysis of Lumenal Proteins of Chloroplast of Wheat using Proteomic Techniques

  • Kamal, Abu Hena Mostafa;Kim, Da-Eun;Oh, Myoung-Won;Chung, Keun-Yook;Cho, Yong-Gu;Kim, Hong-Sig;Song, Beom-Heon;Lee, Chul-Won;Uozumi, Nobuyuki;Choi, Jong-Soon;Cho, Kun;Woo, Sun-Hee
    • 한국자원식물학회:학술대회논문집
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    • 한국자원식물학회 2010년도 정기총회 및 춘계학술발표회
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    • pp.14-14
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    • 2010
  • Plastid proteomics are essential organelles present in virtually all cells in plants and green algae. Plastids are responsible for the synthesis and storage of key molecules required for the basic architecture and functions of plant cells. The proteome of plastid, and in particular of chloroplast, have received significant amounts of attention in recent years. Various fractionation and mass spectrometry (MS) techniques have been applied to catalogue the chloroplast proteome and its sub-organelles compartments. To better understanding the function of the lumenal sub-organelles within the thylakoid network, we have carried out a systematical analysis and identification of the lumenal proteins in the thylakoid of wheat by using Tricine-SDS-PAGE, and LTQ-ESI-FTICR mass spectrometry followed by SWISS-PROT database searching. We isolation and fractionation these membrane from fully developed wheat leaves using a combination of differential and gradient centrifugation couple to high speed ultra-centrifuge. After collecting all proteins to eliminate possible same proteins, we estimated that there are 407 different proteins including chloroplast, chloroplast stroma, lumenal, and thylakoid membrane proteins excluding 20 proteins, which were identified in nucleus, cytoplasm and mitochondria. A combination of these three programs (PSORT, TargetP, TMHMM, and TOPPRED) was found to provide a useful tool for evaluating chloroplast localization, transit peptide, transmembranes, and also could reveal possible alternative processing sites and dual targeting. Finally, we report also sub-cellular location specific protein interaction network using Cytoscape software, which provides further insight into the biochemical pathways of photosynthesis. The present work helps understanding photosynthesis process in wheat at the molecular level and provides a new overview of the biochemical machinery of the thylakoid in wheat.

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미국(美國) 계약법(契約法)하에서 소위 "쉬링크랩라이센스" 계약(契約)에 관한 일고찰(一考察) (A Study on the enforceability of Shrink-wrap License under the Contract Law of USA)

  • 허해관
    • 무역상무연구
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    • 제20권
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    • pp.129-150
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    • 2003
  • Software license agreements, to be useful in the mass market, could not be individually negotiated, and had to be standardized and concise. The software license agreement needs to be presented to the licensee-users in a fashion that would allow for mass distribution of software, also for it to enforceable, that would draw the users' attention to the terms and conditions under which the publisher allowed the use of the software. These needs have been accomplished, with or without fail, through so called the "shrink-wrap licenses" Shrink-wrap licenses purpose to transfer computer softwares to their users by defining the terms and conditions of use of the software without implicating the "first sale doctrine" of the Copyright Act. These shrink-wrap licenses have become essential to the software industry. However, in USA, the law applicable to these licenses has been unclear and unsettled. Courts have struggled to develop a coherent framework governing their enforceability. Meanwhile, the National Conference of Commissioners on Uniform State Laws ("NCCUSL") in USA promulgated the Uniform Computer Information Transaction Act ("UCITA") governing contracts for computer information transaction on July 29, 1999. One clear objective of UCITA was to settle the law governing the enforceability of shrink-wrap licenses. In these respects, this paper first introduces the various forms that shrink-wrap licenses take(at Part II. Section 1.), and explains the main advantages of them(at Part II. Section 2.) Here it shows how shrink-wrap licenses value themselves for both software publishers and users, including that shrink-wrap licenses are a valuable contracting tool because they provide vital information and rights to software users and because they permit the contracting flexibility that is essential for today's software products. Next, this paper describes the current legal framework applicable to shrink-wrap licenses in USA(at Part III). Here it shows that in USA the development of case law governing shrink-wrap licenses occurred in two distinct stages. At first stage, judicial hostility toward shrink-wrap licenses marked such that they were not enforced pursuant to Article 2 of the Uniform Commercial Code. At second stage, courts began to recognize the pervasiveness of shrink-wrap licenses, their indispensability to the rapidly expanding information technology industry, and the urgent need to enforce such licenses in order to maintain low prices for consumers of computer hardware or software, resulting in the recognition of shrink-wrap licenses. Finally, in view of the importance of UCITA, this paper examines how it will affect the enforceability of shrink-wrap licenses(at Part IV). The drafters of UCITA, as well as the scholars and practitioners who have criticized it, agree that it validates shrink-wrap licenses, provided certain procedural protections are afforded to purchasers. These procedural protections include the licensee end-user must (i) manifest his assent to the shrink-wrap license, (ii) have an opportunity to review the shrink-wrap license, (iii) have a right to return the product without costs.

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형광체 결합형 X선 영상검출기의 공간 해상력 몬테카를로 시뮬레이션 (Optical Monte Carlo Simulation on Spatial Resolution of Phosphor Coupled X-ray Imaging Detector)

  • 강상식;김소영;신정욱;허승욱;김재형;남상희
    • 한국전기전자재료학회:학술대회논문집
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    • 한국전기전자재료학회 2007년도 하계학술대회 논문집 Vol.8
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    • pp.328-328
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    • 2007
  • Large area matrix-addressed image detectors are a recent technology for x-ray imaging with medical diagnostic and other applications. The imaging properties of x-ray pixel detectors depend on the quantum efficiency of x-rays, the generated signal of each x-ray photon and the distribution of the generated signal between pixels. In a phosphor coated detector the light signal is generated by electrons captured in the phosphor screen. In our study we simulated the lateral spread distributions for phosphor coupled detector by Monte Carlo simulations. Most simulations of such detectors simplify the setup by only taking the conversion layer into account neglecting behind. The Monte Carlo code MCNPX has been used to simulate the complete interaction and subsequent charge transport of x-ray radiation. This has allowed the analysis of charge sharing between pixel elements as an important limited factor of digital x-ray imaging system. The parameters are determined by lateral distribution of x-ray photons and x-ray induced electrons. The primary purpose of this study was to develop a design tool for the evaluation of geometry factor in the phosphor coupled optical imaging detector. In order to evaluate the spatial resolution for different phosphor material, phosphor geometry we have developed a simulation code. The developed code calculates the energy absorption and spatial distribution based on both the signal from the scintillating layer and the signal from direct detection of x-ray in the detector. We show that internal scattering contributes to the so-called spatial resolution drop of the image detector. Results from the simulation of spatial distribution in a phosphor pixel detector are presented. The spatial resolution can be increased by optimizing pixel size and phosphor thickness.

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How to automatically extract 2D deliverables from BIM?

  • Kim, Yije;Chin, Sangyoon
    • 국제학술발표논문집
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    • The 9th International Conference on Construction Engineering and Project Management
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    • pp.1253-1253
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    • 2022
  • Although the construction industry is changing from a 2D-based to a 3D BIM-based management process, 2D drawings are still used as standards for permits and construction. For this reason, 2D deliverables extracted from 3D BIM are one of the essential achievements of BIM projects. However, due to technical and institutional problems that exist in practice, the process of extracting 2D deliverables from BIM requires additional work beyond generating 3D BIM models. In addition, the consistency of data between 3D BIM models and 2D deliverables is low, which is a major factor hindering work productivity in practice. To solve this problem, it is necessary to build BIM data that meets information requirements (IRs) for extracting 2D deliverables to minimize the amount of work of users and maximize the utilization of BIM data. However, despite this, the additional work that occurs in the BIM process for drawing creation is still a burden on BIM users. To solve this problem, the purpose of this study is to increase the productivity of the BIM process by automating the process of extracting 2D deliverables from BIM and securing data consistency between the BIM model and 2D deliverables. For this, an expert interview was conducted, and the requirements for automation of the process of extracting 2D deliverables from BIM were analyzed. Based on the requirements, the types of drawings and drawing expression elements that require automation of drawing generation in the design development stage were derived. Finally, the method for developing automation technology targeting elements that require automation was classified and analyzed, and the process for automatically extracting BIM-based 2D deliverables through templates and rule-based automation modules were derived. At this time, the automation module was developed as an add-on to Revit software, a representative BIM authoring tool, and 120 rule-based automation rulesets, and the combinations of these rulesets were used to automatically generate 2D deliverables from BIM. Through this, it was possible to automatically create about 80% of drawing expression elements, and it was possible to simplify the user's work process compared to the existing work. Through the automation process proposed in this study, it is expected that the productivity of extracting 2D deliverables from BIM will increase, thereby increasing the practical value of BIM utilization.

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