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GPU accelerated biochemical network simulation

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

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

January 13, 2011 by hgpu

Rapid evaluation and evolution of neural models using graphics card hardware

Thomas F. Clayton, Leena N. Patel, Gareth Leng, Alan F. Murray, Iain A.B. Lindsay

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Tags: Algorithms, Bioinformatics, Biology, CUDA, Evolutionary Computations, nVidia, nVidia GeForce 8800 GTX

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

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

January 11, 2011 by hgpu

Fast binding site mapping using GPUs and CUDA

Bharat Sukhwani, Martin C. Herbordt

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Tags: Bioinformatics, Biology, CUDA, Molecular dynamics, nVidia, Tesla C1060

January 11, 2011 by hgpu

Quality-score guided error correction for short-read sequencing data using CUDA

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

Tags: Bioinformatics, Biology, CUDA, Error recovery, Genetics, nVidia

January 11, 2011 by hgpu

CBESW: sequence alignment on the Playstation 3

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

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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

FPGA acceleration of the phylogenetic likelihood function for Bayesian MCMC inference methods

Stephanie Zierke, Jason Bakos

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Tags: Bioinformatics, Biology, FPGA

January 7, 2011 by hgpu

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

Cheng Ling, Khaled Benkrid, Tsuyoshi Hamada

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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

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

January 4, 2011 by hgpu

Population Parallel GP on the G80 GPU

Denis Robilliard, Virginie Marion-Poty, Cyril Fonlupt

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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

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

December 29, 2010 by hgpu

The GPU on biomedical image processing for color and phenotype analysis

Antonio Ruiz, Manuel Ujaldon, Jose Antonio Andrade

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Tags: Bioinformatics, Image processing, Medicine, nVidia, nVidia GeForce 6800 Ultra, nVidia GeForce 7800 GTX, OpenGL

December 24, 2010 by hgpu

gpu_tracker: Context manager and CLI that tracks the computational-resource-usage of a code block or shell command, particularly the GPU usage

gpu_tracker: Python package for tracking and profiling GPU utilization in both desktop and high-performance computing environments

LOOPer: a polyhedral compiler for expressing fast and portable data parallel algorithms

LOOPer: A Learned Automatic Code Optimizer For Polyhedral Compilers

OpenMC Monte Carlo Code

Performance Portable Monte Carlo Particle Transport on Intel, NVIDIA, and AMD GPUs

Polygeist: C/C++ frontend for MLIR

Retargeting and Respecializing GPU Workloads for Performance Portability

Parallel Gaussian process with kernel approximation in CUDA

Optical flow algorithms for SYCL

SYCL in the edge: performance and energy evaluation for heterogeneous acceleration

OpenMP5-Offload-OpenMC-Intel-PVC

Distributed OpenMP Offloading of OpenMC on Intel GPU MAX Accelerators

See all packages

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high performance computing on graphics processing units: hgpu.org

GPU accelerated biochemical network simulation

Rapid evaluation and evolution of neural models using graphics card hardware

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

Fast binding site mapping using GPUs and CUDA

Quality-score guided error correction for short-read sequencing data using CUDA

CBESW: sequence alignment on the Playstation 3

FPGA acceleration of the phylogenetic likelihood function for Bayesian MCMC inference methods

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

Speeding up subset seed algorithm for intensive protein sequence comparison

Population Parallel GP on the G80 GPU

A SIMD Interpreter for Genetic Programming on GPU Graphics Cards

The GPU on biomedical image processing for color and phenotype analysis

Recent source codes

QArray

Celerity: High-level C++ for Accelerator Clusters

CIFAR-10 Airbench: 94% on CIFAR-10 in 3.29 second

gpu_tracker: Context manager and CLI that tracks the computational-resource-usage of a code block or shell command, particularly the GPU usage

LOOPer: a polyhedral compiler for expressing fast and portable data parallel algorithms

OpenMC Monte Carlo Code

Polygeist: C/C++ frontend for MLIR

Parallel Gaussian process with kernel approximation in CUDA

Optical flow algorithms for SYCL

OpenMP5-Offload-OpenMC-Intel-PVC

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