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CMCpy: Genetic Code-Message Coevolution Models in Python

Peter J. Becich, Brian P. Stark, Harish S. Bhat, David H. Ardell

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Tags: Bioinformatics, Biology, CUDA, nVidia, nVidia GeForce GTX 460, Package, Python

March 31, 2013 by hgpu

GPU-Based Cloud Service for Smith-Waterman algorithm Using Frequency Distance Filtration Scheme

Sheng-Ta Lee, Chun-Yuan Lin, Che Lun Hung

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Tags: Bioinformatics, Biology, Cloud, CUDA, nVidia, Sequence alignment, Smith-Waterman algorithm, Tesla C2050

March 18, 2013 by hgpu

GPU Accelerated Multiple Deoxyribose Nucleic Acid Sequence Parallel Matching

Gang Liao, Qi Sun, Longfei Ma, Zhihui Qin

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Tags: Algorithms, Bioinformatics, Computer science, CUDA, Data Structures and Algorithms, nVidia, nVidia GeForce GTX 680, Sequence matching, Suffix trees

March 18, 2013 by hgpu

GPU based Eulerian Assembly of Genomes

Syed Faraz Mahmood

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Tags: Bioinformatics, Biology, CUDA, Genetics, nVidia, nVidia Quadro FX 5800, Thesis

March 7, 2013 by hgpu

SOAP3-dp: Fast, Accurate and Sensitive GPU-based Short Read Aligner

Ruibang Luo, Thomas Wong, Jianqiao Zhu, Chi-Man Liu, Edward Wu, Lap-Kei Lee, Haoxiang Lin, Wenjuan Zhu, David W. Cheung, Hing-Fung Ting, Siu-Ming Yiu, Chang Yu, Yingrui Li, Ruiqiang Li, Tak-Wah Lam

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Tags: Algorithms, Bioinformatics, Biology, CUDA, Next-Generation sequencing, nVidia, Package, Tesla C2070, Tesla M2050

February 25, 2013 by hgpu

Binary Interval Search: a scalable algorithm for counting interval intersections

Ryan M. Layer, Kevin Skadron, Gabriel Robins, Ira M. Hall, Aaron R. Quinlan

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Tags: Algorithms, Bioinformatics, Biology, Computer science, CUDA, Monte Carlo simulation, nVidia, Package, Sequence alignment

February 6, 2013 by hgpu

Hardware Accelerated Molecular Docking: A Survey

Imre Pechan, Bela Feher

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Tags: Bioinformatics, Biology, CUDA, FPGA, Molecular simulation, nVidia, Tesla C1060

February 6, 2013 by hgpu

Validation of the PyGBe code for Poisson-Boltzmann equation with boundary element methods

Christopher Cooper, Lorena A. Barba

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Tags: Bioinformatics, Biophysics, Boltzmann equation, Computational Physics, Computer science, CUDA, Electrostatics, nVidia, Package, Physics, Poisson Boltzmann, Python, Tesla C2075

January 31, 2013 by hgpu

Faster Algorithms for RNA-folding using the Four-Russians method

Balaji Venkatachalam, Yelena Frid, Dan Gusfield

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Tags: Algorithms, Bioinformatics, Biology, CUDA, nVidia, nVidia GeForce GTX 550 Ti, RNA, Tesla C2070

January 30, 2013 by hgpu

Burrows-Wheeler Aligner: A Parallel Approach

Sheridan Lee Wright

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Tags: Algorithms, Bioinformatics, Biology, CUDA, MPI, nVidia, Sequence alignment, Thesis

January 16, 2013 by hgpu

Acceleration of Selective Cationic Antibacterial Peptides computation: A comparison of FPGA and GPU approaches

D. Garcia-Ordaz, M. Arias-Estrada, M. Nuno-Maganda, C. Polanco, G. Del Rio

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Tags: Bioinformatics, Biology, CUDA, FPGA, nVidia, nVidia GeForce GT 230 M, nVidia GeForce GTX 480, Tesla M2070

January 13, 2013 by hgpu

Optimizations in Bioinformatics using GPU Processing on Binary Data

Manuel Belmadani

Tags: Algorithms, Bioinformatics, Biology, CUDA, nVidia, nVidia GeForce GTX 285

January 8, 2013 by hgpu

Over-synchronization in GPU Programs

profile_util: simple C++ library to report memory, timing, thread affinity

Profile Util library: A quick and easy way to get MPI, OpenMP and GPU runtime information

MaC: Mamba CPU performance predictor

MambaCPU: Enhanced Correlation Mining with State Space Models for CPU Performance Prediction

Mixed-precision finite element kernels

Mixed-precision finite element kernels and assembly: Rounding error analysis and hardware acceleration

SHMT: The Simultaneous and Heterogenous Multithreading project

General-Purpose Computing on Tensor Processors

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high performance computing on graphics processing units: hgpu.org

CMCpy: Genetic Code-Message Coevolution Models in Python

GPU Accelerated Multiple Deoxyribose Nucleic Acid Sequence Parallel Matching

GPU based Eulerian Assembly of Genomes

SOAP3-dp: Fast, Accurate and Sensitive GPU-based Short Read Aligner

Binary Interval Search: a scalable algorithm for counting interval intersections

Hardware Accelerated Molecular Docking: A Survey

Validation of the PyGBe code for Poisson-Boltzmann equation with boundary element methods

Faster Algorithms for RNA-folding using the Four-Russians method

Burrows-Wheeler Aligner: A Parallel Approach

Acceleration of Selective Cationic Antibacterial Peptides computation: A comparison of FPGA and GPU approaches

Optimizations in Bioinformatics using GPU Processing on Binary Data

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Over-synchronization in GPU Programs

profile_util: simple C++ library to report memory, timing, thread affinity

MaC: Mamba CPU performance predictor

Mixed-precision finite element kernels

SHMT: The Simultaneous and Heterogenous Multithreading project

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