• Genomics & Informatics
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• v.18 no.3
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• pp.26.1-26.6
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• 2020

Single-cell RNA sequencing (scRNA-seq) has been widely applied to provide insights into the cell-by-cell expression difference in a given bulk sample. Accordingly, numerous analysis methods have been developed. As it involves simultaneous analyses of many cell and genes, efficiency of the methods is crucial. The conventional cell type annotation method is laborious and subjective. Here we propose a semi-automatic method that calculates a normalized score for each cell type based on user-supplied cell type-specific marker gene list. The method was applied to a publicly available scRNA-seq data of mouse cardiac non-myocyte cell pool. Annotating the 35 t-stochastic neighbor embedding clusters into 12 cell types was straightforward, and its accuracy was evaluated by constructing co-expression network for each cell type. Gene Ontology analysis was congruent with the annotated cell type and the corollary regulatory network analysis showed upstream transcription factors that have well supported literature evidences. The source code is available as an R script upon request.

• Journal of Korean Institute of Industrial Engineers
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• v.22 no.2
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• pp.209-229
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• 1996

Scheduling problems which determine the sequence of jobs are one of the Important issues to many industries. This paper deals with a single-machine job sequencing problem which has complex constraints and an objective function. To solve the problem, an expressive constraint description language and an automatic code generator are developed for our scheduling system. The user just needs to describe the scheduling problem using the constraint description language that allows to express both quantitative and qualitative constraints as well as an objective function in real world semantics. Then, a complete scheduling program based on constraint satisfaction technique is automatically generated through the code generator. Advantage of this approach is that models of the scheduling problems are easily developed and maintained because models ore formulated by using the language which reflects real world semantics.

• Journal of the Korean Association of Oral and Maxillofacial Surgeons
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• v.26 no.1
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• pp.45-52
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• 2000

Nowadays, there are a lot of evidence that mutation of the p53 tumor suppressor gene is one of the most common genetic abnormalities in neoplastic progression. In this study, we analyzed 20 specimens of oral tumors(squamous cell carcinoma 14 cases, ameloblastoma 3 cases, adenoid cystic carcinoma 2 cases, malignant schwannoma 1 case)using polymerase chain reaction and direct sequencing which used an automated DNA sequencer and software for detection of mutations. Polymerase chain reactions were performed with 4 sets of primers encompassing exon 5, 6, 7, 8, and direct sequencing method was employed. The results were as followings. 1. We detected 10 point mutations out of 20 specimens (50%). 2. The genetic alterations included 7 mis-sense mutations resulting in single amino acid subtitutions, 2 silent mutations, 1 non-sense mutations encoding a stop codon. 3. Mutations were mostly in exon 7(7 out of 10 mutations, 70%) and involved codons 225, 234, 235, 236, 238, 247. 4. Therse were 4 cases of $T{\rightarrow}A$ transversion, 2 cases of $C{\rightarrow}A$ transversion, $A{\rightarrow}G$ transition, 1 case of $C{\rightarrow}G$, $T{\rightarrow}G$ transversion respectively. 5. We could find out point mutations more conveniently using PCR - Automated Direct Sequencing method.

• Journal of Korean Institute of Industrial Engineers
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• v.21 no.1
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• pp.119-135
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• 1995

We consider problems of tool loading and scheduling in a flexible manufacturing system (FMS) in which tool transportation constitutes the major portion of material flows. In this type of FMSs, parts are initially assigned to machines and released to the machines according to input sequencing rules. Operations for the parts released to the machines are performed by tools initially loaded onto the machines or provided by an automatic tool transport robot when needed. For an efficient operation of such systems, therefore, we may have to consider loading and scheduling problems for tools in addition to those for parts. In this paper, we consider three problems, part loading, tool loading, and tool scheduling problems with the overall objective of minimizing the makespan. The part loading problem is solved by a method similar to that for the bin packing problem and then a heuristic based on the frequency of tool usage is applied for tool loading. Also suggested are part input sequencing and tool scheduling rules. To show the effectiveness of the overall algorithm suggested here, we compare it with an existing algorithm through a series of computational tests on randomly generated test problems.

• Proceedings of the Korean Society for Bioinformatics Conference
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• 2000.11a
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• pp.83-85
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• 2000

A lot of microbial genome sequencing projects is being done in many genome centers around the world, since the first genome, Haemophilus influenzae, was sequenced in 1995. The deluge of microbial genome sequence data demands new and highly automatic data flow system in order for genome researchers to manage and analyze their own bulky sequence data from low-level to high-level. In such an aspect, we developed the automatic data management system for microbial genome projects, which consists mainly of local database, analysis programs, and user-friendly interface. We designed and implemented the local database for large-scale sequencing projects, which makes systematic and consistent data management and retrieval possible and is tightly coupled with analysis programs and web-based user interface, That is, parsing and storage of the results of analysis programs in local database is possible and user can retrieve the data in any level of data process by means of web-based graphical user interface. Contig assembly, homology search, and ORF prediction, which are essential in genome projects, make analysis programs in our system. All but Contig assembly program are open as public domain. These programs are connected with each other by means of a lot of utility programs. As a result, this system will maximize the efficiency in cost and time in genome research.

• BMB Reports
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• v.29 no.2
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• pp.122-126
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• 1996

A series of oligonucleotides were synthesized by automatic DNA synthesizer. The purity of crude products was checked and their molecular weights determined by matrix assisted laser desorption ionization mass spectrometry (MALDI-MS) with an accuracy of better than 0.05% deviation even without using an internal standard. This mass determining technology in combination with partial digestion of oligonucleotides by 5'- and 3'-exonuclease provides a straightforward and simple method to obtain sequence information of oligonucleotides. The extension of this technology to the sequencing of modified oligonucleotides and genomic DNA and RNA might become possible.

• Proceedings of the Korea Multimedia Society Conference
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• 2002.11b
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• pp.644-648
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• 2002

멀티미디어 서비스를 제공하는 미래의 이동통신 시스템에서는 데이터의 신뢰성 있는 전송을 위해 데이터링크 계층에서 제공하는 프레임 에러율(FER: Frame Error Rates)을 감소시켜야 한다. 이를 위해 라디오링크 프로토콜(RLP: radio link protocol) 계층에서는 ARQ(Automatic Repeat request) 기법을 사용한다. 본 논문에서는 기지국에서 이동 호스트로 전송되는 국부적인 재전송 프레임(Frame)의 순서가 연속된 에러로 인하여 순서가 뒤바뀌고, 이로 인하여 기지국 데이터 링크계층에서 잦은 재전송으로 발생되는 높은 상호지연을 줄이기 위해 개선된 비순서적 재전송 기법을 제안하였다. 제안된 기법은 재전송방법 중 선택적 거절(selective-reject) ARQ의 비순서적 재전송에 수정한 빠른 재전승 기법을 적용하였으며, 기지국과 이동호스트 사이에서 데이터그램(Datagram)의 단편화(fragment)로 인한 링크계층의 Re-Sequencing을 하지 않기 때문에, 종단간 지연된 성능을 향상 시킬 수 있다.

• IE interfaces
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• v.13 no.2
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• pp.195-203
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• 2000

This paper considers the problem of sequencing printed circuit boards(PCBs) on an automatic surface mount device(SMD) placement machine in order to minimize total setup time. Since the total set of component feeders needed by all boards cannot be loaded simultaneously on the magazine, the setup must be made between two successive boards in the sequence. It is assumed that the setup time depends on the number of component feeders to be replaced in the magazine. An important characteristic is that each feeder occupies a different number of slots in the magazine. This problem is equivalent to travelling salesman problem(TSP) except that the distances between two cities, that is, the setup times between two boards, are not known in advance. So, TSP-based heuristics with new distance functions are presented and their performances are compared through various test problems. Computational results indicate that our heuristics outperform existing methods.

• Journal of Korean Society on Water Environment
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• v.33 no.1
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• pp.90-96
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• 2017

Many sewage treatment plants have applied the advanced technology of chemical coagulant system to remove phosporus in Korea. However there are some problems for the injection of optimum coagulant dosage. In order to solve these problems, the research related to the more cost-effective automatic total phosphorus coagulation control system using an EC(Electrical Conductivity) have been in progress. This study was conducted by the same process and operation method as the Lab-scale for public small town sewage treatment plant. First, it confirmed the correlation among the EC, PO4-P and coagulant dosage in the Lab-scale MSBR(Membrane Sequencing Batch Reactor) process. Next, it analyzed that correlation coefficient of EC and the coagulant dosage was 0.92 in the Full-scale MSBR process. As a result, not only T-P removal efficiency was doubled but also it satisfied the effluent water quality standard in a stable manner. In addition, by applying the automatic control system using the EC, compared to the fixed coagulant injection system the coagulant dosage could be reduced by 28%.

• Journal of the Korean Society of Manufacturing Technology Engineers
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• v.24 no.4
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• pp.374-385
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• 2015

In this paper, effective and user friendly CAM software is presented that automatically generates any three dimensional complex toolpaths according to a CAD drawing. In advanced manufacturing, often it is essential to scan the sample following a complex trajectory which consists of short (few microns) and multidirectional moves. The reported CAM software offers constant velocity for all short trajectory elements and provides an efficient shift of tool path direction in sharp corners of a tool trajectory, which is vital for any laser, based precision machining. The software also provides fast modification of tool path, automatic and efficient sequencing of path elements in a complicated tool trajectory, location of reference point and automatic fixing of geometrical errors in imported drawing exchange files (DXF) or DWG format files.