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Study on MPI-based parallel sequence similarity search in the LINUX cluster (클러스터 환경에서의 MPI 기반 병렬 서열 유사성 검색에 관한 연구)

  • Hong, Chang-Bum;Cha, Jeoung-Ho;Lee, Sung-Hoon;Shin, Seung-Woo;Park, Keun-Joon;Park, Keun-Young
    • Journal of the Korea Society of Computer and Information
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    • v.11 no.6 s.44
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    • pp.69-78
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    • 2006
  • In the field of the bioinformatics, it plays an important role in predicting functional information or structure information to search similar sequence in biological DB. Biolrgical sequences have been increased dramatically since Human Genome Project. At this point, because the searching speed for the similar sequence is highly regarded as the important factor for predicting function or structure, the SMP(Sysmmetric Multi-Processors) computer or cluster is being used in order to improve the performance of searching time. As the method to improve the searching time of BLAST(Basic Local Alighment Search Tool) being used for the similarity sequence search, We suggest the nBLAST algorithm performing on the cluster environment in this paper. As the nBLAST uses the MPI(Message Passing Interface), the parallel library without modifying the existing BLAST source code, to distribute the query to each node and make it performed in parallel, it is possible to easily make BLAST parallel without complicated procedures such as the configuration. In addition, with the experiment performing the nBLAST in the 28 nodes of LINUX cluster, the enhanced performance according to the increase in the number of the nodes has been confirmed.

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The e-Business Component Construction based on Distributed Component Specification (분산 컴포넌트 명세를 통한 e-비즈니스 컴포넌트 구축)

  • Kim, Haeng-Gon;Choe, Ha-Jeong;Han, Eun-Ju
    • The KIPS Transactions:PartD
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    • v.8D no.6
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    • pp.705-714
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    • 2001
  • The computing systems of today expanded business trade and distributed business process Internet. More and more systems are developed from components with exactly reusability, independency, and portability. Component based development is focused on advanced concepts rater than passive manipulation or source code in class library. The primary component construction in CBD. However, lead to an additional cost for reconstructing the new component with CBD model. It also difficult to serve component information with rapidly and exactly, which normalization model are not established, frequency user logging in Web caused overload. A lot of difficult issues and aspects of Component Based Development have to be investigated to develop good component-based products. There is no established normalization model which will guarantee a proper treatment of components. This paper elaborates on some of those aspects of web application to adapt user requirement with exactly and rapidly. Distributed components in this paper are used in the most tiny size on network and suggest the network-addressable interface based on business domain. We also discuss the internal and external specifications for grasping component internal and external relations of user requirements to be analyzed. The specifications are stored on Servlets after dividing the information between session and entity as an EJB (Enterprise JavaBeans) that are reusable unit size in business domain. The reusable units are used in business component through query to get business component. As a major contribution, we propose a systems model for registration, auto-arrange, search, test, and download component, which covers component reusability and component customization.

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Subcriticality Evaluation Using the Modified Neutron Source Multiplication Method (개선된 중성자 선원 증배법을 이용한 미임계도 평가)

  • Yoon, Seok-Kyun;Naing, Win;Kim, Myung-Hyun
    • Journal of Energy Engineering
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    • v.16 no.4
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    • pp.155-163
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    • 2007
  • To insure nuclear reactor safety, the reactivity of control rods should be calculated by measuring the criticality of reactor core and it is regularly performed during the annual physics test period. Also, the core criticality should be monitored during the start-up operation to avoid reactivity induced accidents. Many research works on control rod reactivity measurement and subcriticality measurement have been accomplished throughout the world for decades and recently a new method named "Modified Neutron Source Multiplication Method (MNSM)" was proposed in Japan which is known to be improved overcoming limitations of traditional Neutron Source Multiplication Method (NSM). In this study, MNSM was tested in calculation of subcriticalities and in evaluation of application validity using the educational reactor in Kyung Hee University, AGN-201. For this study, a revised nuclear data library and a neutron transport code system TRANSX - PARTISN were established. Correction factors for various control rod positions were produced using the k-effective values and the corresponding flux distributions and adjoint flux distributions. Experimental values of the core criticality were obtained using the neutron count rates of the BF3 proportional counters. The results showed that the expected reactivity worth of control rods by MNSM agreed well with the theoretical values and the correction factors contributed much for this purpose.

The Study of Information Strategy Plan to Design OASIS' Future Model (오아시스(전통의학정보포털)의 미래모형 설계를 위한 정보화전략계획 연구)

  • Yea, Sang-Jun;Kim, Chul;Kim, Jin-Hyun;Kim, Sang-Kyun;Jang, Hyun-Chul;Kim, Ik-Tae;Jang, Yun-Ji;Seong, Bo-Seok;Song, Mi-Young
    • Korean Journal of Oriental Medicine
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    • v.17 no.2
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    • pp.63-71
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    • 2011
  • Objectives : We studied the ISP(information strategy plan) of oasis spanning 5 years. From this study we aimed at total road map to upgrade the service systematically and to carry out the related projects. If we do it as road map, oasis will be the core infra service contributing to the improvement of TKM(traditional korean medicine) research capability. Methods : We carried out 3 step ISP method composed of environmental analysis, current status analysis and future plan. We used paper, report and trend analysis document as base materials and did the survey to get opinions from users and TKM experts. We limited this study to drawing the conceptual design of oasis. Results : From environmental analysis we knew that China and USA built up the largest TM databases. We did the survey to get the activation ways of oasis. And we did the benchmarking on the advanced services through current status analysis. Finally we determined 'maximize the research value based the open TKM knowledge infra' as oasis' vision. And we designed oasis' future system which is composed of service layer, application layer and contents layer. Conclusion : First TKM related documents, research materials, researcher information and standards are merged to elevate the TKM information level. Concretely large scale TKM information infra project such as TKM information classification code development, TKM library network building and CAM research information offering are carried out at the same time.

Numerical Analysis of Runup and Wave Force Acting on Coastal Revetment and Onshore Structure due to Tsunami (해안안벽과 육상구조물에서 지진해일파의 처오름 및 작용파력에 관한 수치해석)

  • Lee, Kwang Ho;Kim, Chang Hoon;Kim, Do Sam;Yeh, Harry;Hwang, Young Tae
    • KSCE Journal of Civil and Environmental Engineering Research
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    • v.29 no.3B
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    • pp.289-301
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    • 2009
  • In this work, wave run-up heights and resultant wave forces on a vertical revetment due to tsunami (solitary wave) are investigated numerically using a numerical wave tank model called CADMAS-SURF (CDIT, 2001. Research and Development of Numerical Wave Channel (CADMAS-SURF). CDIT library, No. 12, Japan.), which is based on a 2-D Navier-Stokes solver, coupled to a volume of fluid (VOF) method. The third order approximate solution (Fenton, 1972. A ninth-order solution for the solitary wave. J. of Fluid Mech., Vol. 53, No.2, pp.257-271) is used to generate solitary waves and implemented in original CADMAS-SURF code. Numerical results of the wave profiles and forces are in good agreements with available experimental data. Using the numerical results, the regression curves determined from the least-square analysis are proposed, which can be used to determine the maximum wave run-up height and force on a vertical revetment due to tsunami. In addition, the capability of CADMAS-SURF is demonstrated for tsunami wave forces acting on an onshore structure using various configuration computations including the variations of the crown heights of the vertical wall and the position of the onshore structure. Based on the numerical results such as water level, velocity field and wave force, the direct effects of tsunami on an onshore structure are discussed.

Evaluation of the CNESTEN's TRIGA Mark II research reactor physical parameters with TRIPOLI-4® and MCNP

  • H. Ghninou;A. Gruel;A. Lyoussi;C. Reynard-Carette;C. El Younoussi;B. El Bakkari;Y. Boulaich
    • Nuclear Engineering and Technology
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    • v.55 no.12
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    • pp.4447-4464
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    • 2023
  • This paper focuses on the development of a new computational model of the CNESTEN's TRIGA Mark II research reactor using the 3D continuous energy Monte-Carlo code TRIPOLI-4 (T4). This new model was developed to assess neutronic simulations and determine quantities of interest such as kinetic parameters of the reactor, control rods worth, power peaking factors and neutron flux distributions. This model is also a key tool used to accurately design new experiments in the TRIGA reactor, to analyze these experiments and to carry out sensitivity and uncertainty studies. The geometry and materials data, as part of the MCNP reference model, were used to build the T4 model. In this regard, the differences between the two models are mainly due to mathematical approaches of both codes. Indeed, the study presented in this article is divided into two parts: the first part deals with the development and the validation of the T4 model. The results obtained with the T4 model were compared to the existing MCNP reference model and to the experimental results from the Final Safety Analysis Report (FSAR). Different core configurations were investigated via simulations to test the computational model reliability in predicting the physical parameters of the reactor. As a fairly good agreement among the results was deduced, it seems reasonable to assume that the T4 model can accurately reproduce the MCNP calculated values. The second part of this study is devoted to the sensitivity and uncertainty (S/U) studies that were carried out to quantify the nuclear data uncertainty in the multiplication factor keff. For that purpose, the T4 model was used to calculate the sensitivity profiles of the keff to the nuclear data. The integrated-sensitivities were compared to the results obtained from the previous works that were carried out with MCNP and SCALE-6.2 simulation tools and differences of less than 5% were obtained for most of these quantities except for the C-graphite sensitivities. Moreover, the nuclear data uncertainties in the keff were derived using the COMAC-V2.1 covariance matrices library and the calculated sensitivities. The results have shown that the total nuclear data uncertainty in the keff is around 585 pcm using the COMAC-V2.1. This study also demonstrates that the contribution of zirconium isotopes to the nuclear data uncertainty in the keff is not negligible and should be taken into account when performing S/U analysis.

Cloning and Transcription Analysis of Sporulation Gene (spo5) in Schizosaccharomyces pombe (Schizosaccharomyces bombe 포자형성 유전자(spo5)의 Cloning 및 전사조절)

  • 김동주
    • The Korean Journal of Food And Nutrition
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    • v.15 no.2
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    • pp.112-118
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    • 2002
  • Sporulation in the fission yeast Schizosaccharomyces pombe has been regarded as an important model of cellular development and differentiation. S. pombe cells proliferate by mitosis and binary fission on growth medium. Deprivation of nutrients especially nitrogen sources, causes the cessation of mitosis and initiates sexual reproduction by matting between two sexually compatible cell types. Meiosis is then followed in a diploid cell in the absence of nitrogen source. DNA fragment complemented with the mutations of sporulation gene was isolated from the S. pombe gene library constructed in the vector, pDB 248' and designated as pDB(spo5)1. We futher analyzed six recombinant plasmids, pDB(spo5)2, pDB(spo5)3, pDB(spo5)4, pDB(spo5)5, pDB (spo5)6, pDB(spo5)7 and found each of these plasmids is able to rescue the spo5-2, spo5-3, spo5-4, spo5-5, spo5-6, spo5-7 mutations, respectively. Mapping of the integrated plasmid into the homologous site of the S. pombe chromosomes demonstrated that pDB(spo5)1, and pDB(spu5)Rl contained the spo5 gene. Transcripts of spo5 gene were analyzed by Northern hybridization. Two transcripts of 3.2 kb and 2.5kb were detected with 5kb Hind Ⅲ fragment containing a part of the spo5 gene as a probe. The small mRNA(2.5kb) appeared only when a wild-type strain was cultured in the absence of nitrogen source in which condition the large mRNA (3.2kb) was produced constitutively. Appearance of a 2.5kb spo5-mRNA depends upon the function of the meil, mei2 and mei3 genes.

Comparison of Deep Learning Frameworks: About Theano, Tensorflow, and Cognitive Toolkit (딥러닝 프레임워크의 비교: 티아노, 텐서플로, CNTK를 중심으로)

  • Chung, Yeojin;Ahn, SungMahn;Yang, Jiheon;Lee, Jaejoon
    • Journal of Intelligence and Information Systems
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    • v.23 no.2
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    • pp.1-17
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    • 2017
  • The deep learning framework is software designed to help develop deep learning models. Some of its important functions include "automatic differentiation" and "utilization of GPU". The list of popular deep learning framework includes Caffe (BVLC) and Theano (University of Montreal). And recently, Microsoft's deep learning framework, Microsoft Cognitive Toolkit, was released as open-source license, following Google's Tensorflow a year earlier. The early deep learning frameworks have been developed mainly for research at universities. Beginning with the inception of Tensorflow, however, it seems that companies such as Microsoft and Facebook have started to join the competition of framework development. Given the trend, Google and other companies are expected to continue investing in the deep learning framework to bring forward the initiative in the artificial intelligence business. From this point of view, we think it is a good time to compare some of deep learning frameworks. So we compare three deep learning frameworks which can be used as a Python library. Those are Google's Tensorflow, Microsoft's CNTK, and Theano which is sort of a predecessor of the preceding two. The most common and important function of deep learning frameworks is the ability to perform automatic differentiation. Basically all the mathematical expressions of deep learning models can be represented as computational graphs, which consist of nodes and edges. Partial derivatives on each edge of a computational graph can then be obtained. With the partial derivatives, we can let software compute differentiation of any node with respect to any variable by utilizing chain rule of Calculus. First of all, the convenience of coding is in the order of CNTK, Tensorflow, and Theano. The criterion is simply based on the lengths of the codes and the learning curve and the ease of coding are not the main concern. According to the criteria, Theano was the most difficult to implement with, and CNTK and Tensorflow were somewhat easier. With Tensorflow, we need to define weight variables and biases explicitly. The reason that CNTK and Tensorflow are easier to implement with is that those frameworks provide us with more abstraction than Theano. We, however, need to mention that low-level coding is not always bad. It gives us flexibility of coding. With the low-level coding such as in Theano, we can implement and test any new deep learning models or any new search methods that we can think of. The assessment of the execution speed of each framework is that there is not meaningful difference. According to the experiment, execution speeds of Theano and Tensorflow are very similar, although the experiment was limited to a CNN model. In the case of CNTK, the experimental environment was not maintained as the same. The code written in CNTK has to be run in PC environment without GPU where codes execute as much as 50 times slower than with GPU. But we concluded that the difference of execution speed was within the range of variation caused by the different hardware setup. In this study, we compared three types of deep learning framework: Theano, Tensorflow, and CNTK. According to Wikipedia, there are 12 available deep learning frameworks. And 15 different attributes differentiate each framework. Some of the important attributes would include interface language (Python, C ++, Java, etc.) and the availability of libraries on various deep learning models such as CNN, RNN, DBN, and etc. And if a user implements a large scale deep learning model, it will also be important to support multiple GPU or multiple servers. Also, if you are learning the deep learning model, it would also be important if there are enough examples and references.

Field Studios of In-situ Aerobic Cometabolism of Chlorinated Aliphatic Hydrocarbons

  • Semprini, Lewts
    • Proceedings of the Korean Society of Soil and Groundwater Environment Conference
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    • 2004.04a
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    • pp.3-4
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    • 2004
  • Results will be presented from two field studies that evaluated the in-situ treatment of chlorinated aliphatic hydrocarbons (CAHs) using aerobic cometabolism. In the first study, a cometabolic air sparging (CAS) demonstration was conducted at McClellan Air Force Base (AFB), California, to treat chlorinated aliphatic hydrocarbons (CAHs) in groundwater using propane as the cometabolic substrate. A propane-biostimulated zone was sparged with a propane/air mixture and a control zone was sparged with air alone. Propane-utilizers were effectively stimulated in the saturated zone with repeated intermediate sparging of propane and air. Propane delivery, however, was not uniform, with propane mainly observed in down-gradient observation wells. Trichloroethene (TCE), cis-1, 2-dichloroethene (c-DCE), and dissolved oxygen (DO) concentration levels decreased in proportion with propane usage, with c-DCE decreasing more rapidly than TCE. The more rapid removal of c-DCE indicated biotransformation and not just physical removal by stripping. Propane utilization rates and rates of CAH removal slowed after three to four months of repeated propane additions, which coincided with tile depletion of nitrogen (as nitrate). Ammonia was then added to the propane/air mixture as a nitrogen source. After a six-month period between propane additions, rapid propane-utilization was observed. Nitrate was present due to groundwater flow into the treatment zone and/or by the oxidation of tile previously injected ammonia. In the propane-stimulated zone, c-DCE concentrations decreased below tile detection limit (1 $\mu$g/L), and TCE concentrations ranged from less than 5 $\mu$g/L to 30 $\mu$g/L, representing removals of 90 to 97%. In the air sparged control zone, TCE was removed at only two monitoring locations nearest the sparge-well, to concentrations of 15 $\mu$g/L and 60 $\mu$g/L. The responses indicate that stripping as well as biological treatment were responsible for the removal of contaminants in the biostimulated zone, with biostimulation enhancing removals to lower contaminant levels. As part of that study bacterial population shifts that occurred in the groundwater during CAS and air sparging control were evaluated by length heterogeneity polymerase chain reaction (LH-PCR) fragment analysis. The results showed that an organism(5) that had a fragment size of 385 base pairs (385 bp) was positively correlated with propane removal rates. The 385 bp fragment consisted of up to 83% of the total fragments in the analysis when propane removal rates peaked. A 16S rRNA clone library made from the bacteria sampled in propane sparged groundwater included clones of a TM7 division bacterium that had a 385bp LH-PCR fragment; no other bacterial species with this fragment size were detected. Both propane removal rates and the 385bp LH-PCR fragment decreased as nitrate levels in the groundwater decreased. In the second study the potential for bioaugmentation of a butane culture was evaluated in a series of field tests conducted at the Moffett Field Air Station in California. A butane-utilizing mixed culture that was effective in transforming 1, 1-dichloroethene (1, 1-DCE), 1, 1, 1-trichloroethane (1, 1, 1-TCA), and 1, 1-dichloroethane (1, 1-DCA) was added to the saturated zone at the test site. This mixture of contaminants was evaluated since they are often present as together as the result of 1, 1, 1-TCA contamination and the abiotic and biotic transformation of 1, 1, 1-TCA to 1, 1-DCE and 1, 1-DCA. Model simulations were performed prior to the initiation of the field study. The simulations were performed with a transport code that included processes for in-situ cometabolism, including microbial growth and decay, substrate and oxygen utilization, and the cometabolism of dual contaminants (1, 1-DCE and 1, 1, 1-TCA). Based on the results of detailed kinetic studies with the culture, cometabolic transformation kinetics were incorporated that butane mixed-inhibition on 1, 1-DCE and 1, 1, 1-TCA transformation, and competitive inhibition of 1, 1-DCE and 1, 1, 1-TCA on butane utilization. A transformation capacity term was also included in the model formation that results in cell loss due to contaminant transformation. Parameters for the model simulations were determined independently in kinetic studies with the butane-utilizing culture and through batch microcosm tests with groundwater and aquifer solids from the field test zone with the butane-utilizing culture added. In microcosm tests, the model simulated well the repetitive utilization of butane and cometabolism of 1.1, 1-TCA and 1, 1-DCE, as well as the transformation of 1, 1-DCE as it was repeatedly transformed at increased aqueous concentrations. Model simulations were then performed under the transport conditions of the field test to explore the effects of the bioaugmentation dose and the response of the system to tile biostimulation with alternating pulses of dissolved butane and oxygen in the presence of 1, 1-DCE (50 $\mu$g/L) and 1, 1, 1-TCA (250 $\mu$g/L). A uniform aquifer bioaugmentation dose of 0.5 mg/L of cells resulted in complete utilization of the butane 2-meters downgradient of the injection well within 200-hrs of bioaugmentation and butane addition. 1, 1-DCE was much more rapidly transformed than 1, 1, 1-TCA, and efficient 1, 1, 1-TCA removal occurred only after 1, 1-DCE and butane were decreased in concentration. The simulations demonstrated the strong inhibition of both 1, 1-DCE and butane on 1, 1, 1-TCA transformation, and the more rapid 1, 1-DCE transformation kinetics. Results of tile field demonstration indicated that bioaugmentation was successfully implemented; however it was difficult to maintain effective treatment for long periods of time (50 days or more). The demonstration showed that the bioaugmented experimental leg effectively transformed 1, 1-DCE and 1, 1-DCA, and was somewhat effective in transforming 1, 1, 1-TCA. The indigenous experimental leg treated in the same way as the bioaugmented leg was much less effective in treating the contaminant mixture. The best operating performance was achieved in the bioaugmented leg with about over 90%, 80%, 60 % removal for 1, 1-DCE, 1, 1-DCA, and 1, 1, 1-TCA, respectively. Molecular methods were used to track and enumerate the bioaugmented culture in the test zone. Real Time PCR analysis was used to on enumerate the bioaugmented culture. The results show higher numbers of the bioaugmented microorganisms were present in the treatment zone groundwater when the contaminants were being effective transformed. A decrease in these numbers was associated with a reduction in treatment performance. The results of the field tests indicated that although bioaugmentation can be successfully implemented, competition for the growth substrate (butane) by the indigenous microorganisms likely lead to the decrease in long-term performance.

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