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BioVLAB-MMIA: A Cloud Environment for microRNA and mRNA Integrated Analysis (MMIA) on Amazon EC2
Hyungro Lee,Youngik Yang,Heejoon Chae,Seungyoon Nam,Donghoon Choi,Tangchaisin, P.,Herath, C.,Marru, S.,Nephew, K. P.,Sun Kim IEEE 2012 IEEE transactions on nanobioscience Vol.11 No.3
<P>MicroRNAs, by regulating the expression of hundreds of target genes, play critical roles in developmental biology and the etiology of numerous diseases, including cancer. As a vast amount of microRNA expression profile data are now publicly available, the integration of microRNA expression data sets with gene expression profiles is a key research problem in life science research. However, the ability to conduct genome-wide microRNA-mRNA (gene) integration currently requires sophisticated, high-end informatics tools, significant expertise in bioinformatics and computer science to carry out the complex integration analysis. In addition, increased computing infrastructure capabilities are essential in order to accommodate large data sets. In this study, we have extended the BioVLAB cloud workbench to develop an environment for the integrated analysis of microRNA and mRNA expression data, named BioVLAB-MMIA. The workbench facilitates computations on the Amazon EC2 and S3 resources orchestrated by the XBaya Workflow Suite. The advantages of BioVLAB-MMIA over the web-based MMIA system include: 1) readily expanded as new computational tools become available; 2) easily modifiable by re-configuring graphic icons in the workflow; 3) on-demand cloud computing resources can be used on an “as needed” basis; 4) distributed orchestration supports complex and long running workflows asynchronously. We believe that BioVLAB-MMIA will be an easy-to-use computing environment for researchers who plan to perform genome-wide microRNA-mRNA (gene) integrated analysis tasks.</P>
Convergence Characteristics of Upwind Method for Modified Artificial Compressibility Method
Hyungro Lee,Seungsoo Lee 한국항공우주학회 2011 International Journal of Aeronautical and Space Sc Vol.12 No.4
This paper investigates the convergence characteristics of the modified artificial compressibility method proposed by Turkel. In particular, a focus is mode on the convergence characteristics due to variation of the preconditioning factor (αu) and the artificial compressibility (β) in conjunction with an upwind method. For the investigations, a code using the modified artificial compressibility is developed. The code solves the axisymmetric incompressible Reynolds averaged Navier-Stokes equations. The cell-centered finite volume method is used in conjunction with Roe’s approximate Riemann solver for the inviscid flux, and the central difference discretization is used for the viscous flux. Time marching is accomplished by the approximated factorizationalternate direction implicit method. In addition, Menter’s k-ω shear stress transport turbulence model is adopted for analysis of turbulent flows. Inviscid, laminar, and turbulent flows are solved to investigate the accuracy of solutions and convergence behavio r in the modified artificial compressibility method. The possible reason for loss of robustness of the modified artificial compressibility method with αu >1.0 is given.
강제조화운동을 이용한 SDM의 세로 및 방향 안정성 미계수 예측
이형로(Hyungro Lee),이승수(Seungsoo Lee),조창열(Chang-Yeol Joh) 한국항공우주학회 2012 韓國航空宇宙學會誌 Vol.40 No.11
본 논문에서는 SDM 형상의 세로와 방향의 안정성 미계수를 예측하였다. 피치와 요 방향에 대한 강제조화 진동운동을 이용하여 정적 및 동적 미계수를 한 번에 계산하였다. 계산은 비정상 해석을 위한 이중시간 적분법을 적용한 3차원 Euler 해석자를 사용하여 수행하였다. 본 연구에서는 마하수뿐만 아니라 다양한 운동 변수에 따른 미계수를 예측하였다. 예측된 결과는 이전에 발표된 수치적, 실험적 연구 결과들과 비교하여 검증하였다. This paper presents the computations of the longitudinal and directional stability derivatives for the SDM(Standard Dynamic Model). The static and dynamic derivatives are evaluated at once using forced harmonic oscillations in the pitch and yaw directions. For the numerical simulations, a 3-D Euler solver that uses a dual time stepping method for unsteady time accurate simulations is applied. This work investigates the variation of the derivatives in terms of the Mach number and the several motion parameters. Good agreement of the pitch and yaw stability derivatives with previously published numerical results and experimental results are observed.
전산유체역학을 이용한 비행체의 피치와 롤 동안정 미계수 예측
이형로(Hyungro Lee),공효준(Hyojoon Gong),김범수(BeomSoo Kim),이승수(Seungsoo Lee) 한국항공우주학회 2012 韓國航空宇宙學會誌 Vol.40 No.5
본 논문에서는 전산유체역학을 이용하여 3차원 비행체 형상에 대한 동안정 미계수를 예측하였다. 피치에 대한 미계수는 피치방향의 조화진동운동을 통하여 계산하였고 롤 감쇠계수는 비관성 좌표계에 대한 정상해석을 통하여 계산하였다. 계산은 Basic Finner와 SDM 형상에 대해 수행했으며 다른 연구자의 실험적/수치적 결과와 비교하였다. 유동 계산을 위해 비관성 좌표계와 관성 좌표계에서 모두 사용할 수 있는 3차원 Euler 해석자를 개발하였다. 시간 정확성을 유지한 비정상 해석을 위해 이중시간적분법을 적용하였다. 동안정 미계수 계산 결과는 다른 수치 및 실험적 연구 결과들과 잘 일치하는 것을 알 수 있었다. This paper presents computations of the dynamic derivatives of three dimensional flight vehicle configurations using CFD. The pitch dynamic derivatives are computed from the pitch sinusoidal motion, while the roll damping is computed based on steady state calculation using a non-inertial frame method. The Basic Finner and the SDM(Standard Dynamic Model) are chosen for the benchmark tests against other numerical and experimental results. For the flow calculations, a 3-D Euler solver that can be run both on the non-inertial frame and on the inertial frame is developed. A dual-time stepping method is applied for the unsteady time accurate simulations. A good agreement of pitch-roll dynamic derivatives with previously published numerical results and the experimental results is observed.
Numerical simulation of flows around axisymmetric inlet with bleed regions
Einkeun Kwak,Hyungro Lee,이승수 대한기계학회 2010 JOURNAL OF MECHANICAL SCIENCE AND TECHNOLOGY Vol.24 No.12
A numerical simulation of flows in an axisymmetric supersonic inlet with bleed regions is performed. An existing code which solves the Reynolds Averaged Navier-Stokes equations and the two-equation turbulence model equations is converted into an axisymmetric code. In addition, a bleed boundary condition model has been applied to the code. In this paper, the modified code is validated by comparing numerical results against experimental data and other computational results for flows on a bump and over an oblique shock with bleed region. Using the code, numerical simulation is performed for the flows in an inlet with multiple bleed regions.