high performance computing on graphics processing units: hgpu.org

hgpu.org » Applications » Biology

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

FluoroSim: A Visual Problem-Solving Environment for Fluorescence Microscopy

Cory W. Quammen, Alvin C. Richardson, Julian Haase, Benjamin D. Harrison, Russell M. Taylor, Kerry S. Bloom

View

Download (PDF)

Source codes

Tags: Algorithms, Biology, CUDA, Image generation, Microscopy, nVidia, nVidia GeForce 8800 GTX, OpenGL, Package

March 2, 2011 by hgpu

STOCHSIMGPU: Parallel stochastic simulation for the Systems Biology Toolbox 2 for MATLAB

Guido Klingbeil, Radek Erban, Mike Giles, Philip K. Maini

View

Download (PDF)

Source codes

Tags: Bioinformatics, Biology, CUDA, nVidia, nVidia GeForce 8800, Package, Stochastic simulation

February 28, 2011 by hgpu

Size Matters: Space/Time Tradeoffs to Improve GPGPU Applications Performance

Abdullah Gharaibeh, Matei Ripeanu

View

Download (PDF)

Source codes

Tags: Bioinformatics, Biology, Computational biology, CUDA, nVidia, nVidia GeForce 8800 GTX, Package, Sequence alignment, Short read mapping, Suffix trees

February 27, 2011 by hgpu

Next-generation acceleration and code optimization for light transport in turbid media using GPUs

Erik Alerstam, William C. Yip Lo, Tianyi D. Han, Jonathan Rose, Stefan Andersson-Engels, Lothar Lilge

View

Download (PDF)

Source codes

Tags: Biology, CUDA, Monte Carlo simulation, nVidia, nVidia GeForce GTX 280, nVidia GeForce GTX 295, nVidia GeForce GTX 480, Optics, Package

February 9, 2011 by hgpu

GPU accelerated biochemical network simulation

Yanxiang Zhou, Juliane Liepe, Xia Sheng, Michael P. H. Stumpf, Chris Barnes

View

Download (PDF)

Source codes

Tags: Bioinformatics, Biology, CUDA, GPU cluster, nVidia, Package, Tesla C2050

January 13, 2011 by hgpu

Automated image alignment for 2D gel electrophoresis in a high-throughput proteomics pipeline

Andrew W. Dowsey, Michael J. Dunn, Guang-Zhong Z. Yang

View

Download (PDF)

Source codes

Tags: Bioinformatics, Biology, Cg, Image alignment, nVidia, nVidia GeForce 6800 Ultra, Package

January 11, 2011 by hgpu

CBESW: sequence alignment on the Playstation 3

Adrianto Wirawan, Chee Keong K. Kwoh, Nim Tri T. Hieu, Bertil Schmidt

View

Download (PDF)

Source codes

Tags: Algorithms, Bioinformatics, Biology, BLAST, Cell processor, CUDA, nVidia, nVidia GeForce 8800 GTX, Package, Playstation, Sequence alignment, Smith-Waterman algorithm

January 8, 2011 by hgpu

Population Parallel GP on the G80 GPU

Denis Robilliard, Virginie Marion-Poty, Cyril Fonlupt

View

Download (PDF)

Source codes

Tags: Bioinformatics, Biology, CUDA, Genetics, nVidia, nVidia GeForce 8800 GTX, Package

December 29, 2010 by hgpu

Real-world comparison of CPU and GPU implementations of SNPrank: a network analysis tool for GWAS

Nicholas A. Davis, Ahwan Pandey, B. A. McKinney

View

Download (PDF)

Source codes

Tags: Bioinformatics, Biology, CUDA, Genetics, Medicine, nVidia, Package, Tesla M1060

December 13, 2010 by hgpu

SWPS3 – fast multi-threaded vectorized Smith-Waterman for IBM Cell/B.E. and x86/SSE2

Adam Szalkowski, Christian Ledergerber, Philipp Kraehenbuehl, Christophe Dessimoz

View

Download (PDF)

Source codes

Tags: Biology, Cell processor, CUDA, nVidia, nVidia GeForce 8800 GTX, Optimization, Package, Sequence alignment, Smith-Waterman algorithm

December 12, 2010 by hgpu

Coccinelle: a C code transformation engine using SmPL for matches, refactorings, and bug fixing

Advances in Semantic Patching for HPC-oriented Refactorings with Coccinelle

DuoReduce: MLIR's benchmark

Hardware-Assisted Software Testing and Debugging for Heterogeneous Computing

Shamrock: Multi-GPU hydrodynamics for astrophysics

The Shamrock code: I- Smoothed Particle Hydrodynamics on GPUs

LLMPerf: GPU Performance Modeling meets Large Language Models

Hercules: A Compiler for Productive Programming of Heterogeneous Systems

* * *

high performance computing on graphics processing units: hgpu.org

Packages

MrBayes on a Graphics Processing Unit

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

FluoroSim: A Visual Problem-Solving Environment for Fluorescence Microscopy

STOCHSIMGPU: Parallel stochastic simulation for the Systems Biology Toolbox 2 for MATLAB

Size Matters: Space/Time Tradeoffs to Improve GPGPU Applications Performance

Next-generation acceleration and code optimization for light transport in turbid media using GPUs

GPU accelerated biochemical network simulation

Automated image alignment for 2D gel electrophoresis in a high-throughput proteomics pipeline

CBESW: sequence alignment on the Playstation 3

Population Parallel GP on the G80 GPU

Real-world comparison of CPU and GPU implementations of SNPrank: a network analysis tool for GWAS

SWPS3 – fast multi-threaded vectorized Smith-Waterman for IBM Cell/B.E. and x86/SSE2

Recent source codes

Coccinelle: a C code transformation engine using SmPL for matches, refactorings, and bug fixing

DuoReduce: MLIR's benchmark

Shamrock: Multi-GPU hydrodynamics for astrophysics

LLMPerf: GPU Performance Modeling meets Large Language Models

Hercules: A Compiler for Productive Programming of Heterogeneous Systems

Celerity Runtime: High-level C++ for Accelerator Clusters

wgpy: WebGL accelerated numpy-compatible array library for web browser

Microbenchmarking OpenMP target offload with Catch2

SUperman: Highly Efficient Permanent Computation Library

TransCL: An Automatic CUDA-to-OpenCL Programs Transformation Framework

Most viewed papers (last 30 days)