high performance computing on graphics processing units: hgpu.org

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hgpu.org » Applications » Biology

Performance evaluation of image processing algorithms on the GPU

Daniel Castano-Diez, Dominik Moser, Andreas Schoenegger, Sabine Pruggnaller, Achilleas S S. Frangakis

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Tags: Biology, CUDA, Image processing, Medicine, nVidia, nVidia Quadro FX 5600, Pattern recognition, Tomography

December 7, 2010 by hgpu

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

Implementation and performance evaluation of reconstruction algorithms on graphics processors

D. Castanodiez, H. Mueller, A. Frangakis

Tags: Biology, Electron microscopy, Image processing

December 6, 2010 by hgpu

Hierarchical clustering of gene expression profiles with graphics hardware acceleration

Q. Zhang, Y. Zhang

Tags: Biology, Genetics, Pattern recognition

December 4, 2010 by hgpu

Locality and parallelism optimization for dynamic programming algorithm in bioinformatics

Guangming Tan, Shengzhong Feng, Ninghui Sun

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Tags: Algorithms, Bioinformatics, Biology, Programming techniques

December 2, 2010 by hgpu

ClawHMMER: A Streaming HMMer-Search Implementation

Daniel R. Horn, Mike Houston, Pat Hanrahan

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Tags: ATI, ATI Radeon X800, Bioinformatics, Biology, Brook, nVidia, nVidia GeForce 6800 Ultra, nVidia GeForce 7800 GTX, Pattern Search

November 30, 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 Massively Parallel Architecture for Bioinformatics

Gerd Pfeiffer, Stefan Baumgart, Jan Schroder, Manfred Schimmler

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Tags: Algorithms, Bioinformatics, Biology, FPGA, MapReduce

November 27, 2010 by hgpu

Parallel reconstruction of neighbor-joining trees for large multiple sequence alignments using CUDA

Yongchao Liu, Bertil Schmidt, Douglas L. Maskell

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Tags: Bioinformatics, Biology, CUDA, nVidia, nVidia GeForce GTX 280, Sequence alignment, Smith-Waterman algorithm

November 27, 2010 by hgpu

Implications of the Turing completeness of reaction-diffusion models, informed by GPGPU simulations on an XBox 360: cardiac arrhythmias, re-entry and the Halting problem

Simon Scarle

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Tags: Biology, Heart, Medicine, Visualization, Xbox 360

November 27, 2010 by hgpu

CUDA-MEME: Accelerating Motif Discovery in Biological Sequences Using CUDA-enabled Graphics Processing Units

Yongchao Liu, Bertil Schmidt, Weiguo Liu, Douglas L. Maskell

Tags: Biology, CUDA, nVidia, nVidia GeForce GTX 280, Pattern recognition

November 27, 2010 by hgpu

Awesome LLM-Driven Kernel Generation

Towards Automated Kernel Generation in the Era of LLMs

PhysProver: Advancing Automatic Theorem Proving for Physics

ParaCodex: A Profiling-Guided Autonomous Coding Agent for Reliable Parallel Code Generation and Translation

SeedFold: Scaling Biomolecular Structure Prediction

Tilus: A Tile-Level GPU Kernel Programming Language

Tilus: A Tile-Level GPGPU Programming Language for Low-Precision Computation

Memory-Efficient Acceleration of Block Low-Rank Foundation Models on Resource Constrained GPUs

BoltzGen:Toward Universal Binder Design

CUDA-L2: Surpassing cuBLAS Performance for Matrix Multiplication through Reinforcement Learning

cuPilot: A Strategy-Coordinated Multi-agent Framework for CUDA Kernel Evolution

MATLAB Tensor Core models

Accurate Models of NVIDIA Tensor Cores

See all packages

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high performance computing on graphics processing units: hgpu.org

Applications

Performance evaluation of image processing algorithms on the GPU

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

Implementation and performance evaluation of reconstruction algorithms on graphics processors

Hierarchical clustering of gene expression profiles with graphics hardware acceleration

Locality and parallelism optimization for dynamic programming algorithm in bioinformatics

ClawHMMER: A Streaming HMMer-Search Implementation

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

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

A Massively Parallel Architecture for Bioinformatics

Parallel reconstruction of neighbor-joining trees for large multiple sequence alignments using CUDA

Implications of the Turing completeness of reaction-diffusion models, informed by GPGPU simulations on an XBox 360: cardiac arrhythmias, re-entry and the Halting problem

CUDA-MEME: Accelerating Motif Discovery in Biological Sequences Using CUDA-enabled Graphics Processing Units

Recent source codes

Awesome LLM-Driven Kernel Generation

PhysProver: Advancing Automatic Theorem Proving for Physics

ParaCodex: A Profiling-Guided Autonomous Coding Agent for Reliable Parallel Code Generation and Translation

SeedFold: Scaling Biomolecular Structure Prediction

Tilus: A Tile-Level GPU Kernel Programming Language

Memory-Efficient Acceleration of Block Low-Rank Foundation Models on Resource Constrained GPUs

BoltzGen:Toward Universal Binder Design

CUDA-L2: Surpassing cuBLAS Performance for Matrix Multiplication through Reinforcement Learning

cuPilot: A Strategy-Coordinated Multi-agent Framework for CUDA Kernel Evolution

MATLAB Tensor Core models

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