high performance computing on graphics processing units: hgpu.org

hgpu.org » Bioinformatics

A Parallel Gibbs Sampling Algorithm for Motif Finding on GPU

Linbin Yu, Yun Xu

Tags: Bioinformatics, Biology, CUDA, nVidia, Sequence matching

April 9, 2011 by hgpu

On accelerating iterative algorithms with CUDA: A case study on Conditional Random Fields training algorithm for biological sequence alignment

Zhihui Du, Zhaoming Yin, Wenjie Liu, D. Bader

Tags: Bioinformatics, Biology, CUDA, nVidia, Sequence alignment

April 8, 2011 by hgpu

A Hybrid Computational Grid Architecture for Comparative Genomics

A. Singh, Chen Chen, Weiguo Liu, W. Mitchell, B. Schmidt

Tags: Bioinformatics, Biology, Genetics, Sequence alignment

April 6, 2011 by hgpu

The optimization of parallel Smith-Waterman sequence alignment using on-chip memory of GPGPU

Qian Zhang, Hong An, Gu Liu, Wenting Han, Ping Yao, Mu Xu, Xiaoqiang Li

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

April 4, 2011 by hgpu

Optimizing Smith-Waterman algorithm on Graphics Processing Unit

A. Khalafallah, H.F. Elbabb, O. Mahmoud, A. Elshamy

Tags: Bioinformatics, Biology, OpenCL, Sequence alignment, Smith-Waterman algorithm

April 1, 2011 by hgpu

Implementation of Smith-Waterman Algorithm in OpenCL for GPUs

Dzmitry Razmyslovich, Guillermo Marcus, Markus Gipp, Marc Zapatka, Andreas Szillus

View

Download (PDF)

Tags: Bioinformatics, Biology, CUDA, nVidia, nVidia GeForce GTX 260, nVidia GeForce GTX 480, OpenCL, Poster, Sequence alignment, Smith-Waterman algorithm

March 31, 2011 by hgpu

CuHMMer: A load-balanced CPU-GPU cooperative bioinformatics application

Ping Yao, Hong An, Mu Xu, Gu Liu, Xiaoqiang Li, Yaobin Wang, Wenting Han

View

Download (PDF)

Tags: Bioinformatics, Biology, CUDA, nVidia, nVidia GeForce 8800 GTX, Pattern Search

March 29, 2011 by hgpu

A GPU Implementation of Fast Parallel Markov Clustering in Bioinformatics Using EllPACK-R Sparse Data Format

A. Bustamam, K. Burrage, N.A. Hamilton

Tags: Bioinformatics, Biology, CUDA, nVidia

March 25, 2011 by hgpu

MrBayes on a Graphics Processing Unit

Jianfu Zhou, Xiaoguang Liu, Douglas S. Stones, Qiang Xie, Gang Wang

Source codes

Tags: Bayesian, Bioinformatics, Biology, CUDA, nVidia, nVidia GeForce GTX 480, Package

March 18, 2011 by hgpu

GBOOST : A GPU-based tool for detecting gene-gene interactions in genome-wide case control studies

Ling Sing S. Yung, Can Yang, Xiang Wan, Weichuan Yu

Source codes

Tags: Bioinformatics, Biology, Genetics, nVidia, nVidia GeForce GTX 285, Package

March 12, 2011 by hgpu

GPU-RMAP: Accelerating Short-Read Mapping on Graphics Processors

Ashwin M. Aji, Liqing Zhang, Wu C. Feng

Tags: Bioinformatics, Biology, Next-Generation sequencing, nVidia

March 9, 2011 by hgpu

A tile-based parallel Viterbi algorithm for biological sequence alignment on GPU with CUDA

Zhihui Du, Zhaoming Yin, David A. Bader

View

Download (PDF)

Tags: Bioinformatics, Biology, CUDA, nVidia, nVidia GeForce 9800 GTX, Sequence alignment

March 7, 2011 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

Superpipeline: A Universal Approach for Reducing GPU Memory Usage in Large Models

EnergyUCB-Bandit

Online Energy Optimization in GPUs: A Multi-Armed Bandit Approach

See all packages

* * *

high performance computing on graphics processing units: hgpu.org

A Parallel Gibbs Sampling Algorithm for Motif Finding on GPU

On accelerating iterative algorithms with CUDA: A case study on Conditional Random Fields training algorithm for biological sequence alignment

A Hybrid Computational Grid Architecture for Comparative Genomics

The optimization of parallel Smith-Waterman sequence alignment using on-chip memory of GPGPU

Optimizing Smith-Waterman algorithm on Graphics Processing Unit

Implementation of Smith-Waterman Algorithm in OpenCL for GPUs

CuHMMer: A load-balanced CPU-GPU cooperative bioinformatics application

A GPU Implementation of Fast Parallel Markov Clustering in Bioinformatics Using EllPACK-R Sparse Data Format

MrBayes on a Graphics Processing Unit

GBOOST : A GPU-based tool for detecting gene-gene interactions in genome-wide case control studies

GPU-RMAP: Accelerating Short-Read Mapping on Graphics Processors

A tile-based parallel Viterbi algorithm for biological sequence alignment on GPU with CUDA

Recent source codes

Kokkidio: Kokkos+Eigen - write fast, readable multi-platform code

LLaMA-Inference-Bench

MATAR

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

Superpipeline: A Universal Approach for Reducing GPU Memory Usage in Large Models

EnergyUCB-Bandit

Most viewed papers (last 30 days)