high performance computing on graphics processing units: hgpu.org

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SW#db: GPU-accelerated exact sequence similarity database search

Matija Korpar, Martin Sosic, Dino Blazeka, Mile Sikic

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Tags: Algorithms, Biology, CUDA, Databases, Next-Generation sequencing, nVidia, nVidia GeForce GTX 690, nVidia GeForce GTX 780, Package, Smith-Waterman algorithm

January 16, 2015 by hgpu

Bayesian neural networks for detecting epistasis in genetic association studies

Andrew L Beam, Alison Motsinger-Reif, Jon Doyle

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Tags: Bayesian, Biology, CUDA, CULA, Neural networks, nVidia, Package, Python

December 15, 2014 by hgpu

MEGAHIT: An ultra-fast single-node solution for large and complex metagenomics assembly via succinct de Bruijn graph

Dinghua Li, Chi-Man Liu, Ruibang Luo, Kunihiko Sadakane, Tak-Wah Lam

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Tags: Biology, CUDA, Genomics, nVidia, Package, Tesla K40

September 29, 2014 by hgpu

Convex Clustering: An Attractive Alternative to Hierarchical Clustering

Gary K. Chen, Eric Chi, John Ranola, Kenneth Lange

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Tags: Algorithms, Bioinformatics, Biology, Cluster analysis, Clustering, Genomics, Hierarchical clustering, nVidia, OpenCL, Package, Tesla C2050

September 9, 2014 by hgpu

Simulating spiking neural networks on massively parallel graphical processing units using a code generation approach with GeNN

Esin Yavuz, James Turner, Thomas Nowotny

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Tags: Bioinformatics, Biology, Code generation, CUDA, Neural networks, Neuroscience, nVidia, Package, Tesla C2070

July 28, 2014 by hgpu

An efficient parallel algorithm for accelerating computational protein design

Yichao Zhou, Wei Xu, Bruce R. Donald, Jianyang Zeng

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Tags: Algorithms, Bioinformatics, Biology, CUDA, Java, nVidia, Package, Tesla K20

June 23, 2014 by hgpu

GPU-BSM: A GPU-Based Tool to Map Bisulfite-Treated Reads

Andrea Manconi, Alessandro Orro, Emanuele Manca, Giuliano Armano, Luciano Milanesi

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Tags: Bioinformatics, Biology, CUDA, Genetics, nVidia, nVidia GeForce GTX 480, Package, Python, Sequence alignment, Tesla K10, Tesla K20

May 25, 2014 by hgpu

GAMUT: GPU accelerated microRNA analysis to uncover target genes through CUDA-miRanda

Shuang Wang, Jihoon Kim, Xiaoqian Jiang, Stefan F Brunner, Lucila Ohno-Machado

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Tags: Bioinformatics, Biology, CUDA, nVidia, Package, RNA, Smith-Waterman algorithm, Tesla M2090

May 10, 2014 by hgpu

Bayesian Neural Networks for Genetic Association Studies of Complex Disease

Andrew L. Beam, Alison Motsinger-Reif, Jon Doyle

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Tags: Bayesian, Biology, CUDA, Machine learning, Neural networks, nVidia, Package, Python

April 17, 2014 by hgpu

QuickProbs – A Fast Multiple Sequence Alignment Algorithm Designed for Graphics Processors

Adam Gudys, Sebastian Deorowicz

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Tags: ATI, ATI Radeon HD 7970, Bioinformatics, Biology, nVidia, nVidia GeForce GTX 480, nVidia GeForce GTX 580, nVidia GeForce GTX 680, OpenCL, Package, Sequence alignment

March 4, 2014 by hgpu

MICA: A fast short-read aligner that takes full advantage of Intel Many Integrated Core Architecture (MIC)

Sze-Hang Chan, Jeanno Cheung, Edward Wu, Heng Wang, Chi-Man Liu, Xiaoqian Zhu, Shaoliang Peng, Ruibang Luo, Tak-Wah Lam

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Tags: Bioinformatics, Biology, Intel Xeon Phi, Package

February 21, 2014 by hgpu

Parallel implementation of 3D protein structure similarity searches using a GPU and the CUDA

Dariusz Mrozek, Milosz Brozek, Bozena Malysiak-Mrozek

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Tags: Algorithms, Bioinformatics, Biology, CUDA, nVidia, nVidia GeForce GTX 285, nVidia GeForce GTX 560 Ti, Package, Tesla C1060

February 4, 2014 by hgpu

HPCTransCompile: An AI Compiler Generated Dataset for High-Performance CUDA Transpilation and LLM Preliminary Exploration

Efficient Graph Embedding at Scale: Optimizing CPU-GPU-SSD Integration

Can Large Language Models Predict Parallel Code Performance?

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high performance computing on graphics processing units: hgpu.org

Applications

SW#db: GPU-accelerated exact sequence similarity database search

Bayesian neural networks for detecting epistasis in genetic association studies

MEGAHIT: An ultra-fast single-node solution for large and complex metagenomics assembly via succinct de Bruijn graph

Convex Clustering: An Attractive Alternative to Hierarchical Clustering

Simulating spiking neural networks on massively parallel graphical processing units using a code generation approach with GeNN

An efficient parallel algorithm for accelerating computational protein design

GPU-BSM: A GPU-Based Tool to Map Bisulfite-Treated Reads

GAMUT: GPU accelerated microRNA analysis to uncover target genes through CUDA-miRanda

Bayesian Neural Networks for Genetic Association Studies of Complex Disease

QuickProbs – A Fast Multiple Sequence Alignment Algorithm Designed for Graphics Processors

MICA: A fast short-read aligner that takes full advantage of Intel Many Integrated Core Architecture (MIC)

Parallel implementation of 3D protein structure similarity searches using a GPU and the CUDA

Recent source codes

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