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Fast Parallel Image Registration on CPU and GPU for Diagnostic Classification of Alzheimer’s Disease

Denis P. Shamonin, Esther E. Bron, Boudewijn P. Lelieveldt, Marion Smits, Stefan Klein, Marius Staring

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Tags: Bioinformatics, Image processing, Image registration, Medicine, MRI, Neuroscience, nVidia, nVidia GeForce GTX 480, OpenCL

January 2, 2014 by hgpu

HUGO: Hierarchical mUlti-reference Genome cOmpression for aligned reads

Pinghao Li, Xiaoqian Jiang, Shuang Wang, Jihoon Kim, Hongkai Xiong, Lucila Ohno-Machado

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Tags: Algorithms, Bioinformatics, Biology, Clustering, Compression, CUDA, nVidia, Package, Sequence alignment, Tesla M2090

December 27, 2013 by hgpu

Accelerating Pairwise DNA Sequence Alignment using the CUDA Compatible GPU

H. Khaled, R. El Gohary, N. L. Badr, H. M. Faheem

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Tags: Algorithms, Bioinformatics, Biology, CUDA, nVidia, nVidia GeForce GT 540 M, Sequence alignment, Smith-Waterman algorithm

December 22, 2013 by hgpu

Efficient Multi-GPU Computation of All-Pairs Shortest Paths

Hristo Djidjev, Sunil Thulasidasan, Guillaume Chapuis, Rumen Andonov, Dominique Lavenier

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Tags: Algorithms, Bioinformatics, Biology, CUDA, GPU cluster, nVidia, Tesla C2090

December 18, 2013 by hgpu

Exploiting parallel features of modern computer architectures in bioinformatics

Guillaume Chapuis

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Tags: Algorithms, Bioinformatics, Biology, CUDA, Genetics, nVidia, Path problems, Tesla C2050, Tesla C2090, Thesis

December 16, 2013 by hgpu

Graphics Processing Unit-Accelerated Quantitative Trait Loci Detection

Guillaume Chapuis, Olivier Filangi, Dominique Lavenier, Jean Michel J. M. Elsen, Pascale Leroy

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Tags: Bioinformatics, Biology, CUDA, nVidia, Tesla C2050

November 16, 2013 by hgpu

Accelerating calculations of RNA secondary structure partition functions using GPUs

Harry A Stern, David H Mathews

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Tags: Bioinformatics, Biology, CUDA, nVidia, Package, RNA, Tesla M2050

November 11, 2013 by hgpu

High-performance Dynamic Programming on FPGAs with OpenCL

Sean O. Settle

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Tags: Bioinformatics, Computer science, FPGA, Heterogeneous systems, OpenCL, RNA, Smith-Waterman algorithm

October 29, 2013 by hgpu

cudaMap: a GPU accelerated program for gene expression connectivity mapping

Darragh G McArt, Peter Bankhead, Philip D Dunne, Manuel Salto-Tellez, Peter Hamilton, Shu-Dong Zhang

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

October 17, 2013 by hgpu

High performance sequence mining using pairwise statistical significance

Yuhong Zhang, Feng Chen

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Tags: Algorithms, Bioinformatics, Biology, CUDA, nVidia, Package, Tesla C2050

October 12, 2013 by hgpu

Regional Heritability Advanced Complex Trait Analysis for GPU and Traditional Parallel Architectures

L. Cebamanos, A. Gray, I. Stewart, A. Tenesa

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

October 12, 2013 by hgpu

Enabling the use of Heterogeneous Computing for Bioinformatics

Ramakrishna Bijanapalli Chakri

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Tags: Bioinformatics, Biology, CUDA, FPGA, Heterogeneous systems, nVidia, nVidia GeForce GTX 580, Smith-Waterman algorithm, Thesis

October 8, 2013 by hgpu

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

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

pyATF: The Auto-Tuning Framework (ATF) in Python

pyATF: Constraint-Based Auto-Tuning in Python

TritonBench: Benchmarking Large Language Model Capabilities for Generating Triton Operators

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high performance computing on graphics processing units: hgpu.org

Fast Parallel Image Registration on CPU and GPU for Diagnostic Classification of Alzheimer’s Disease

HUGO: Hierarchical mUlti-reference Genome cOmpression for aligned reads

Accelerating Pairwise DNA Sequence Alignment using the CUDA Compatible GPU

Efficient Multi-GPU Computation of All-Pairs Shortest Paths

Exploiting parallel features of modern computer architectures in bioinformatics

Graphics Processing Unit-Accelerated Quantitative Trait Loci Detection

Accelerating calculations of RNA secondary structure partition functions using GPUs

High-performance Dynamic Programming on FPGAs with OpenCL

cudaMap: a GPU accelerated program for gene expression connectivity mapping

High performance sequence mining using pairwise statistical significance

Regional Heritability Advanced Complex Trait Analysis for GPU and Traditional Parallel Architectures

Enabling the use of Heterogeneous Computing for Bioinformatics

Recent source codes

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

pyATF: The Auto-Tuning Framework (ATF) in Python

TritonBench: Benchmarking Large Language Model Capabilities for Generating Triton Operators

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