• 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.

• Biomedical Science Letters
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• v.10 no.4
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• pp.523-528
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• 2004

The core factor of the study is integrated environment based PC-Cluster system and high speed access rate up to 155 Mbps, continuous collection system for bioinformatics information at home and abroad. The results of the study are establishment and stabilization of information and communication infrastructure, establishment and stabilization of high performance computer network up to 155 Mbps, development of PC-Cluster system with 32 nodes, a parallelized BLAST on Cluster system, which can provides scalable speedup in terms of response time, and development of collection and search system for bioinformatics information.

• Journal of Biomedical Engineering Research
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• v.25 no.6
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• pp.617-621
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• 2004

In recent, researchers in the field of Bioinformatics need to analyze thousands of genome sequences efficiently according to introduce of new analysis methods and technologies such as genome expression microchip. This rapid growth in the field of bio-engineering needs computing resources to analyze rapidly for genome sequences, but it does not introduce the computing resources due to an enormous investment expense. The core factor of this study is integrated environment based PC-Cluster system & high speed access rate up to 155Mbps, continuous collection system for bio-information at home and abroad. The results of the study are establishment & stabilization of information and communication infrastructure, establishment & stabilization of high performance computer network up to 155Mbps, development of PC-Cluster system with 32 nodes, a parallel BLAST on Cluster system, which can provides scalable speedup in terms of response time, and development of collection & search system for bio-information.

• Bioinformatics and Biosystems
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• v.2 no.2
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• pp.37-45
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• 2007

생물정보학은 컴퓨터를 이용하여 방대한 양의 생물학적 데이터를 처리하고 그 결과를 분석하는 학문으로서 IT의 고속성장과 맞물려 점차 그 활용도를 넓혀가고 있다. 특히 의학, 생명과학 연구에 사용되는 데이터는 그 종류도 다양하고 크기가 매우 큰 것이 일반적인데, 이의 처리를 위해서는 고속 네트워크가 바탕이 된 그리드-컴퓨팅(Grid-Computing) 기술 접목이 필연적이다. 고속 네트워크 기술의 발전은 슈퍼컴퓨터를 대체해 컴퓨터 풀 내에 분산된 시스템들을 하나로 묶을 수 있는 그리드-컴퓨팅 분야를 선도하고 있다. 최근 생물정보학 분야에서도 이처럼 발전된 고성능 분산 컴퓨팅 기술을 이용하여 데이터의 신속한 처리와 관리의 효율성을 증대시키고 있는 추세이다. 그리드-컴퓨팅 기술은 크게 데이터 가공을 위한 응용 프로그램 개발과 데이터 관리를 위한 데이터베이스 구축으로 구분 지을 수 있다. 전자에 해당하는 생물정보 연구용 프로그램들은 mpiBLAST, ClustalW-MPI와 같은 MSA서열정렬 프로그램들을 꼽을 수 있으며, BioSimGrid, Taverna와 같은 프로젝트는 그리드-데이터베이스 (Grid-Database)기술을 바탕으로 개발되었다. 본 고에서는 미지의 생명현상을 탐구하고 연구하기 위하여 현재까지 개발된 그리드-컴퓨팅 환경과 의생명과학 연구를 위한 응용 프로그램들, 그리고 그리드-데이터베이스 기술 등을 소개한다.

• Asian Pacific Journal of Cancer Prevention
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• v.15 no.12
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• pp.4773-4780
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• 2014

Background: To investigate the effects of small interference RNA (siRNA) targeting BCR/ABL mRNA on proliferation and apoptosis in the K562 human chronic myeloid leukemia (CML) cell line and to provide a theoretical rationale and experimental evidence for its potential clinical application for anti-CML treatment. Materials and Methods: The gene sequence for BCR/ABL mRNA was found from the GeneBank. The target gene site on the BCR/ABL mRNA were selected according to Max-Planck-Institute (MPI) and rational siRNA design rules, the secondary structure of the candidate targeted mRNA was predicted, the relevant thermodynamic parameters were analyzed, and the targeted gene sequences were compared with BLAST to eliminate any sequences with significant homology. Inhibition of proliferation was evaluated by MTT assay and colony-formation inhibiting test. Apoptosis was determined by flow cytometry (FCM) and the morphology of apoptotic cells was identified by Giemsa-Wright staining. Western blotting was used to analyze the expression of BCR/ABL fusion protein in K562 cells after siRNA treatment. Results: The mRNA local secondary structure calculated by RNA structure software, and the optimal design of specific siRNA were contributed by bioinformatics rules. Five sequences of BCR/ABL siRNAs were designed and synthesized in vitro. Three sequences, siRNA1384, siRNA1276 and siRNA1786, which showed the most effective inhibition of K562 cell growth, were identified among the five candidate siRNAs, with a cell proliferative inhibitory rate nearly 50% after exposure to 12.5nmol/L~50nmol/L siRNA1384 for 24,48 and 72 hours. The 50% inhibitory concentrations ($IC_{50}$) of siRNA1384, siRNA1276 and siRNA1786 for 24hours were 46.6 nmol/L, 59.3 nmol/L and 62.6 nmol/L, respectively, and 65.668 nmol/L, 76.6 nmol/L, 74.4 nmol/L for 72 hours. The colony-formation inhibiting test also indicated that, compared with control, cell growth of siRNA treated group was inhibited. FCM results showed that the rate of cell apoptosis increased 24 hours after transfecting siRNA. The results of annexinV/PI staining indicated that the rate of apoptosis imcreased (1.53%, 15.3%, 64.5%, 57.5% and 21.5%) following treamtne with siRNAs (siRNA34, siRNA372, siRNA1384, siRNA1276 and siRNA1786). Morphological analysis showed td typical morphologic changes of apoptosis such as shrunken, fragmentation nucleus as well as "apoptotic bodies" after K562 cell exposure to siRNA. Western blot analysis showed that BCR/ABL protein was reduced sharply after a single dose of 50nmol/L siRNA transfection. Conclusions: Proliferation of K562 cells was remarkbly inhibited by siRNAs (siRNA1384, siRNA1276 and siRNA1786) in a concentration-dependent manner in vitro, with effective induction of apoptosis at a concentration of 50 nmol/L. One anti-leukemia mechanism in K562 cells appeared that BCR/ABL targeted protein was highly down-regulated. The siRNAs (siRNA1384, siRNA1276 and siRNA1786) may prove valuable in the treatment of CML.