Parallelization of Nullspace Algorithm for the computation of metabolic pathways [0.03%]
代谢途径的空穴算法并行化计算
Dimitrije Jevremović,Cong T Trinh,Friedrich Srienc et al.
Dimitrije Jevremović et al.
Elementary mode analysis is a useful metabolic pathway analysis tool in understanding and analyzing cellular metabolism, since elementary modes can represent metabolic pathways with unique and minimal sets of enzyme-catalyzed reactions of a...
GPU computing with Kaczmarz's and other iterative algorithms for linear systems [0.03%]
基于Kaczmarz及其他迭代算法的GPU线性系统求解方法研究
Joseph M Elble,Nikolaos V Sahinidis,Panagiotis Vouzis
Joseph M Elble
The graphics processing unit (GPU) is used to solve large linear systems derived from partial differential equations. The differential equations studied are strongly convection-dominated, of various sizes, and common to many fields, includi...
Multilevel Summation of Electrostatic Potentials Using Graphics Processing Units [0.03%]
基于图形处理器的多级静电势求和方法
David J Hardy,John E Stone,Klaus Schulten
David J Hardy
Physical and engineering practicalities involved in microprocessor design have resulted in flat performance growth for traditional single-core microprocessors. The urgent need for continuing increases in the performance of scientific applic...
Optimizing Data Intensive GPGPU Computations for DNA Sequence Alignment [0.03%]
优化数据密集型的一般用途GPU计算以进行DNA序列比对
Cole Trapnell,Michael C Schatz
Cole Trapnell
MUMmerGPU uses highly-parallel commodity graphics processing units (GPU) to accelerate the data-intensive computation of aligning next generation DNA sequence data to a reference sequence for use in diverse applications such as disease geno...
RNAVLab: A virtual laboratory for studying RNA secondary structures based on grid computing technology [0.03%]
基于网格计算技术的探究RNA二级结构的虚拟实验室(RNAVLab)
Michela Taufer,Ming-Ying Leung,Thamar Solorio et al.
Michela Taufer et al.
As ribonucleic acid (RNA) molecules play important roles in many biological processes including gene expression and regulation, their secondary structures have been the focus of many recent studies. Despite the computing power of supercompu...
Guest Editors' Introduction, Special Issue on High-Performance Computational Biology [0.03%]
高性能计算生物学专题编辑导语
David A Bader,Srinivas Aluru
David A Bader
Explicit Design of FPGA-Based Coprocessors for Short-Range Force Computations in Molecular Dynamics Simulations [0.03%]
基于FPGA的用于分子动力学模拟中短程力计算的片上系统显式设计
Yongfeng Gu,Tom Vancourt,Martin C Herbordt
Yongfeng Gu
FPGA-based acceleration of molecular dynamics simulations (MD) has been the subject of several recent studies. The short-range force computation, which dominates the execution time, is the primary focus. Here we combine: a high level of FPG...
Martin C Herbordt,Josh Model,Bharat Sukhwani et al.
Martin C Herbordt et al.
Approximate string matching is fundamental to bioinformatics and has been the subject of numerous FPGA acceleration studies. We address issues with respect to FPGA implementations of both BLAST- and dynamic-programming- (DP) based methods. ...