• Journal of Microbiology and Biotechnology
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• v.23 no.1
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• pp.99-105
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• 2013

In this study, nitrous oxide ($N_2O$) emission was compared between the operations of two different sequencing batch reactors, conventional sequencing batch reactor (CNVSBR) and simultaneous nitrification and denitrification sequencing batch reactor (SND-SBR), using synthetic wastewater. The CNV-SBR consisted of anoxic (denitrification) and aerobic phases, whereas the SND-SBR consisted of a microaerobic (low dissolved oxygen concentration) phase, which was achieved by intermittent aeration for simultaneous nitrification and denitrification. The CNV-SBR emitted 3.9 mg of $N_2O$-N in the denitrification phase and 1.6 mg of $N_2O$-N in the nitrification phase, resulting in a total emission of 5.5mg from 432mg of $NH_4^+$-N input. In contrast, the SND-SBR emitted 26.2mg of $N_2O$-N under the microaerobic condition, which was about 5 times higher than the emission obtained with the CNV-SBR at the same $NH_4^+$-N input. From the $N_2O$ yield based on $NH_4^+$-N input, the microaerobic condition produced the highest yield (6.1%), followed by the anoxic (0.9%) and aerobic (0.4%) conditions. It is thought that an appropriate dissolved oxygen level is critical for reducing $N_2O$ emission during nitrification and denitrification at wastewater treatment plants.

• Genomics & Informatics
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• v.16 no.4
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• pp.29.1-29.5
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• 2018

Hybrid capture-based targeted sequencing is being used increasingly for genomic variant profiling in tumor patients. Unique molecular index (UMI) technology has recently been developed and helps to increase the accuracy of variant calling by minimizing polymerase chain reaction biases and sequencing errors. However, UMI-adopted targeted sequencing data analysis is slightly different from the methods for other types of omics data, and its pipeline for variant calling is still being optimized in various study groups for their own purposes. Due to this provincial usage of tools, our group built an analysis pipeline for global application to many studies of targeted sequencing generated with different methods. First, we generated hybrid capture-based data using genomic DNA extracted from tumor tissues of colorectal cancer patients. Sequencing libraries were prepared and pooled together, and an 8-plexed capture library was processed to the enrichment step before 150-bp paired-end sequencing with Illumina HiSeq series. For the analysis, we evaluated several published tools. We focused mainly on the compatibility of the input and output of each tool. Finally, our laboratory built an analysis pipeline specialized for UMI-adopted data. Through this pipeline, we were able to estimate even on-target rates and filtered consensus reads for more accurate variant calling. These results suggest the potential of our analysis pipeline in the precise examination of the quality and efficiency of conducted experiments.

• Journal of Institute of Control, Robotics and Systems
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• v.10 no.3
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• pp.280-285
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• 2004

This paper is concerned with the modeling and identification of sequencing batch reactor (SBR) via genetic algorithm based polynomial neural network (GA-based PNN). The model describes a biological SBR used in the wastewater treatment process fur nitrogen removal. A conventional polynomial neural network (PNN) is applied to construct a predictive model of SBR process fur nitrogen removal before. But the performances of PNN depend strongly on the number of input variables available to the model, the number of input variables and type (order) of the polynomials to each node. They must be fixed by the designer in advance before the architecture is constructed. So the trial and error method must go with heavy computation burden and low efficiency. To alleviate these problems, we propose GA-based PNN. The order of the polynomial, the number of input variables, and the optimum input variables are encoded as a chromosome and fitness of each chromosome is computed. Simulation results have shown that the complex SBR process can be modeled reasonably well by the present scheme with a much simpler structure compared with the conventional PNN model.

• 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.

• Industrial Engineering and Management Systems
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• v.15 no.1
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• pp.11-18
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• 2016

This paper considers a scheduling problem in a flexible job shop with a reconfigurable manufacturing cell. The flexible job shop has both operation and routing flexibilities, which can be represented in the form of a multiple process plan, i.e. each part can be processed through alternative operations, each of which can be processed on alternative machines. The scheduling problem has three decision variables: (a) selecting operation/machine pairs for each part; (b) sequencing of parts to be fed into the reconfigurable manufacturing cell; and (c) sequencing of the parts assigned to each machine. Due to the reconfigurable manufacturing cell's ability of adjusting the capacity, functionality and flexibility to the desired levels, the priority scheduling approach is proposed in which the three decisions are made at the same time by combining operation/machine selection rules, input sequencing rules and part sequencing rules. To show the performances of various rule combinations, simulation experiments were done on various instances generated randomly using the experiences of the manufacturing experts, and the results are reported for the objectives of minimizing makespan, mean flow time and mean tardiness, respectively.

• Proceedings of the Korean Operations and Management Science Society Conference
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• 1996.04a
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• pp.737-740
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• 1996

This paper suggests a boltzman machine neural network model to determine model input sequences in line balancing process of mixed model assembly line. We first present a proper energy function, next determine the value of parameters using simulation process.

• 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 Korea Society for Industrial Systems Conference
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• 1999.05a
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• pp.145-153
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• 1999

We consider a Direct Input Output Manufacturing System(DIOMS) which has a munber of machine centers placed along a built-in Automated Storage/Retrieval System(AS/RS). The Storage/Retrieval (S/R) machine handles parts placed on pallets for the machine centers located at either one or both sides of the As/Rs. This report studies the operational aspect of DIOMS and determines the optimal operating policy by combining computer simulation and genetic algorithm. The operational problem includes: input sequencing control, dispatching rule of the S/R machine, machine center-based part type selection rule, and storage assignment policy. For each operating policy, several different policies are considered based on the known research results. In this report, using the computer simulation and genetic algorithm we suggest a method which gives the optimal configuration of operating policies within reasonable computation time.

• Journal of Korean Society of Industrial and Systems Engineering
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• v.23 no.61
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• pp.127-135
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• 2000

This paper provides a new method of initializing neurons used in self-organizing neural networks and sequencing input nodes for applying to Euclidean traveling salesman problem. We use a general property that in any optimal solution for Euclidean traveling salesman problem, vertices located on the convex hull are visited in the order in which they appear on the convex hull boundary. We composite input nodes as number of convex hulls and initialize neurons as shape of the external convex hull. And then adapt input nodes as the convex hull unit and all convex hulls are adapted as same pattern, clockwise or counterclockwise. As a result of our experiments, we obtain l∼3 % improved solutions and these solutions can be used for initial solutions of any global search algorithms.

• Molecules and Cells
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• v.44 no.8
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• pp.602-612
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• 2021

DNA methylation is an important epigenetic mechanism affecting genome structure, gene regulation, and the silencing of transposable elements. Cell- and tissue-specific methylation patterns are critical for differentiation and development in eukaryotes. Dynamic spatiotemporal methylation data in these cells or tissues is, therefore, of great interest. However, the construction of bisulfite sequencing libraries can be challenging if the starting material is limited or the genome size is small, such as in Arabidopsis. Here, we describe detailed methods for the purification of Arabidopsis embryos at all stages, and the construction of comprehensive bisulfite libraries from small quantities of input. We constructed bisulfite libraries by releasing embryos from intact seeds, using a different approach for each developmental stage, and manually picking single-embryo with microcapillaries. From these libraries, reliable Arabidopsis methylome data were collected allowing, on average, 11-fold coverage of the genome using as few as five globular, heart, and torpedo embryos as raw input material without the need for DNA purification step. On the other hand, purified DNA from as few as eight bending torpedo embryos or a single mature embryo is sufficient for library construction when RNase A is treated before DNA extraction. This method can be broadly applied to cells from different tissues or cells from other model organisms. Methylome construction can be achieved using a minimal amount of input material using our method; thereby, it has the potential to increase our understanding of dynamic spatiotemporal methylation patterns in model organisms.