high performance computing on graphics processing units: hgpu.org

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GPU-MEME: Using Graphics Hardware to Accelerate Motif Finding in DNA Sequences

Chen Chen, Bertil Schmidt, Liu Weiguo, Wolfgang Muller-Wittig

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Tags: Bioinformatics, Biology, GLSL, nVidia, nVidia GeForce 8800 GTX, OpenGL, Package, Pattern recognition

December 6, 2010 by hgpu

GPU-BLAST: Using graphics processors to accelerate protein sequence alignment

Panagiotis D. Vouzis, Nikolaos V. Sahinidis

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Tags: Bioinformatics, Biology, BLAST, CUDA, nVidia, Package, Sequence alignment, Tesla C2050

November 30, 2010 by hgpu

Highly accelerated feature detection in proteomics data sets using modern graphics processing units

Rene Hussong, Barbara Gregorius, Andreas Tholey, Andreas Hildebrandt

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Tags: Bioinformatics, Biology, CUDA, nVidia, Package, Tesla C870

November 28, 2010 by hgpu

A Parallel Algorithm for Error Correction in High-Throughput Short-Read Data on CUDA-Enabled Graphics Hardware

Haixiang Shi, Bertil Schmidt, Weiguo Liu, Wolfgang Muller-Wittig

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Tags: Biology, Computer science, CUDA, Error recovery, nVidia, Package

November 22, 2010 by hgpu

Parallel Position Weight Matrices Algorithms

Mathieu Giraud, Jean-Stephane Varre

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Tags: Biology, Computer science, CUDA, nVidia, nVidia GeForce 8800, nVidia GeForce GTX 280, Package

November 22, 2010 by hgpu

GPU-enabled FREALIGN: Accelerating single particle 3D reconstruction and refinement in Fourier space on graphic processors

Xueming Li, Nikolaus Grigorieff, Yifan Cheng

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Tags: Biology, CUDA, Electron microscopy, Image reconstruction, nVidia, Package

November 18, 2010 by hgpu

Fast free-form deformation using graphics processing units

Marc Modat, Gerard R. Ridgway, Zeike A. Taylor, Manja Lehmann, Josephine Barnes, David J. Hawkes, Nick C. Fox, Sebastien Ourselin

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Tags: Biology, CUDA, Image processing, Medicine, nVidia, nVidia GeForce 8800 GTX, Package

November 17, 2010 by hgpu

permGPU: Using graphics processing units in RNA microarray association studies

Ivo Shterev, Sin H. Jung, Stephen George, Kouros Owzar

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Tags: Bioinformatics, Biology, CUDA, Genetics, nVidia, nVidia GeForce GTX 280, Package, RNA

November 17, 2010 by hgpu

ABC-SysBio–approximate Bayesian computation in Python with GPU support

Juliane Liepe, Chris Barnes, Erika Cule, Kamil Erguler, Paul Kirk, Tina Toni, Michael P. H. Stumpf

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Tags: Bioinformatics, Biology, CUDA, nVidia, Package, Python

November 9, 2010 by hgpu

Multifactor dimensionality reduction for graphics processing units enables genome-wide testing of epistasis in sporadic ALS

Casey S. Greene, Nicholas A. Sinnott-Armstrong, Daniel S. Himmelstein, Paul J. Park, Jason H. Moore, Brent T. Harris

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Tags: Bioinformatics, Biology, CUDA, Genetics, nVidia, nVidia GeForce GTX 295, Package

November 7, 2010 by hgpu

CUDASW++ 2.0: enhanced Smith-Waterman protein database search on CUDA-enabled GPUs based on SIMT and virtualized SIMD abstractions

Yongchao Liu, Bertil Schmidt, Douglas Maskell

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Tags: Bioinformatics, Biology, Computational biology, CUDA, nVidia, nVidia GeForce GTX 280, nVidia GeForce GTX 295, Package, Smith-Waterman algorithm

November 6, 2010 by hgpu

Automatic fitting of spiking neuron models to electrophysiological recordings

Cyrille Rossant, Dan F. Goodman, Jonathan Platkiewicz, Romain Brette

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Tags: Adaptive threshold, Biology, CUDA, Distributed computing, Neuroscience, nVidia, nVidia GeForce GTX 295, Optimization, Package

November 6, 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

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high performance computing on graphics processing units: hgpu.org

Packages

GPU-MEME: Using Graphics Hardware to Accelerate Motif Finding in DNA Sequences

GPU-BLAST: Using graphics processors to accelerate protein sequence alignment

Highly accelerated feature detection in proteomics data sets using modern graphics processing units

A Parallel Algorithm for Error Correction in High-Throughput Short-Read Data on CUDA-Enabled Graphics Hardware

Parallel Position Weight Matrices Algorithms

GPU-enabled FREALIGN: Accelerating single particle 3D reconstruction and refinement in Fourier space on graphic processors

Fast free-form deformation using graphics processing units

permGPU: Using graphics processing units in RNA microarray association studies

ABC-SysBio–approximate Bayesian computation in Python with GPU support

Multifactor dimensionality reduction for graphics processing units enables genome-wide testing of epistasis in sporadic ALS

CUDASW++ 2.0: enhanced Smith-Waterman protein database search on CUDA-enabled GPUs based on SIMT and virtualized SIMD abstractions

Automatic fitting of spiking neuron models to electrophysiological recordings

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

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