high performance computing on graphics processing units: hgpu.org

hgpu.org » Applications » Biology

Accelerating phase unwrapping and affine transformations for optical quadrature microscopy using CUDA

Perhaad Mistry, Sherman Braganza, David Kaeli, Miriam Leeser

View

Download (PDF)

Tags: Biology, CUDA, Genetics, Image processing, nVidia, nVidia GeForce 8800 GTX

January 6, 2011 by hgpu

A parameterisable and scalable Smith-Waterman algorithm implementation on CUDA-compatible GPUs

Cheng Ling, Khaled Benkrid, Tsuyoshi Hamada

View

Download (PDF)

Tags: Bioinformatics, Biology, Computational biology, CUDA, nVidia, nVidia GeForce 8800 GTX, Sequence alignment, Smith-Waterman algorithm

January 4, 2011 by hgpu

Speeding up subset seed algorithm for intensive protein sequence comparison

Van Hoa Nguyen, Dominique Lavenier

View

Download (PDF)

Tags: Bioinformatics, Biology, CUDA, nVidia, nVidia GeForce 8800 GTX, Sequence alignment

January 4, 2011 by hgpu

Towards Large-Scale Molecular Dynamics Simulations on Graphics Processors

Joseph E. Davis, Adnan Ozsoy, Sandeep Patel, Michela Taufer

View

Download (PDF)

Tags: Biology, Chemistry, CUDA, Molecular dynamics, nVidia, nVidia GeForce 9800 GX2, nVidia GeForce GTX 280, nVidia Quadro FX 5600

January 3, 2011 by hgpu

Analysis of a Computational Biology Simulation Technique on Emerging Processing Architectures

Jeremy S. Meredith, Sadaf R. Alam, Jeffrey S. Vetter

View

Download (PDF)

Tags: Biology, Cell processor, Cg, Computational biology, Molecular dynamics, nVidia, nVidia GeForce 7900 GTX

January 2, 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

A SIMD Interpreter for Genetic Programming on GPU Graphics Cards

William B. Langdon, Wolfgang Banzhaf

View

Download (PDF)

Tags: Bioinformatics, Biology, DirectX, Genetics, nVidia, nVidia GeForce 8800 GTX, OpenGL

December 29, 2010 by hgpu

Design and implementation of the Smith-Waterman algorithm on the CUDA-compatible GPU

Yuma Munekawa, Fumihiko Ino, Kenichi Hagihara

View

Download (PDF)

Tags: Bioinformatics, Biology, CUDA, nVidia, nVidia GeForce 8800 GTX, Smith-Waterman algorithm

December 22, 2010 by hgpu

Long time-scale simulations of in vivo diffusion using GPU hardware

Elijah Roberts, John E. Stone, Leonardo Sepulveda, Wen-Mei W. Hwu, Zaida Luthey-Schulten

View

Download (PDF)

Tags: Bioinformatics, Biology, CUDA, Distributed computing, nVidia, nVidia GeForce GTX 280, nVidia Quadro FX 5600

December 18, 2010 by hgpu

A New Parallel Method of Smith-Waterman Algorithm on a Heterogeneous Platform

Bo Chen, Yun Xu, Jiaoyun Yang, Haitao Jiang

View

Download (PDF)

Tags: Biology, CUDA, nVidia, nVidia GeForce 9800 GT, Sequence alignment, Smith-Waterman algorithm

December 17, 2010 by hgpu

GPU Accelerated RNA Folding Algorithm

Guillaume Rizk, Dominique Lavenier

View

Download (PDF)

Tags: Algorithms, Bioinformatics, Biology, CUDA, nVidia, nVidia GeForce GTX 280, Tesla C870

December 17, 2010 by hgpu

Integrative multicellular biological modeling: a case study of 3D epidermal development using GPU algorithms

Scott Christley, Briana Lee, Xing Dai, Qing Nie

View

Download (PDF)

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

December 15, 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

Applications

Accelerating phase unwrapping and affine transformations for optical quadrature microscopy using CUDA

A parameterisable and scalable Smith-Waterman algorithm implementation on CUDA-compatible GPUs

Speeding up subset seed algorithm for intensive protein sequence comparison

Towards Large-Scale Molecular Dynamics Simulations on Graphics Processors

Analysis of a Computational Biology Simulation Technique on Emerging Processing Architectures

Population Parallel GP on the G80 GPU

A SIMD Interpreter for Genetic Programming on GPU Graphics Cards

Design and implementation of the Smith-Waterman algorithm on the CUDA-compatible GPU

Long time-scale simulations of in vivo diffusion using GPU hardware

A New Parallel Method of Smith-Waterman Algorithm on a Heterogeneous Platform

GPU Accelerated RNA Folding Algorithm

Integrative multicellular biological modeling: a case study of 3D epidermal development using GPU algorithms

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)