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Efficient parallel algorithms for maximum-density segment problem

Xue Wang, Fasheng Qiu, S.K. Prasad, Guantao Chen

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Tags: Bioinformatics, Biology, CUDA, nVidia, nVidia GeForce GTX 280, Presentation, Sequence alignment

March 7, 2011 by hgpu

FluoroSim: A Visual Problem-Solving Environment for Fluorescence Microscopy

Cory W. Quammen, Alvin C. Richardson, Julian Haase, Benjamin D. Harrison, Russell M. Taylor, Kerry S. Bloom

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Tags: Algorithms, Biology, CUDA, Image generation, Microscopy, nVidia, nVidia GeForce 8800 GTX, OpenGL, Package

March 2, 2011 by hgpu

STOCHSIMGPU: Parallel stochastic simulation for the Systems Biology Toolbox 2 for MATLAB

Guido Klingbeil, Radek Erban, Mike Giles, Philip K. Maini

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Tags: Bioinformatics, Biology, CUDA, nVidia, nVidia GeForce 8800, Package, Stochastic simulation

February 28, 2011 by hgpu

CUDAlign: using GPU to accelerate the comparison of megabase genomic sequences

Edans Flavius O. Sandes, Alba Cristina M.A. de Melo

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

February 27, 2011 by hgpu

Size Matters: Space/Time Tradeoffs to Improve GPGPU Applications Performance

Abdullah Gharaibeh, Matei Ripeanu

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Tags: Bioinformatics, Biology, Computational biology, CUDA, nVidia, nVidia GeForce 8800 GTX, Package, Sequence alignment, Short read mapping, Suffix trees

February 27, 2011 by hgpu

HexServer: an FFT-based protein docking server powered by graphics processors

Gary Macindoe, Lazaros Mavridis, Vishwesh Venkatraman, Marie-Dominique Devignes, David W. Ritchie

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Tags: Bioinformatics, Biology, CUDA, FFT, Molecular simulation, nVidia, Tesla C1060

February 25, 2011 by hgpu

A Resource-Efficient Computing Paradigm for Computational Protein Modeling Applications

Yaohang Li, Douglas Wardell, Vincent Freeh

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Tags: Algorithms, Biology, Molecular dynamics

February 24, 2011 by hgpu

Probing biomolecular machines with graphics processors

James C. Phillips, John E. Stone

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Tags: Biology, Biomolecules, CUDA, GPU cluster, Molecular simulation, nVidia, OpenCL, Review, Tesla S1070

February 23, 2011 by hgpu

Accelerating the Stochastic Simulation Algorithm

David Jenkins, Gregory D. Peterson

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Tags: Biology, CUDA, Monte Carlo simulation, MPI, nVidia, Stochastic simulation, Tesla C870

February 21, 2011 by hgpu

A massively parallel framework using P systems and GPUs

Jose M. Cecilia, Gines D. Guerrero, Jose M. Garcia, Miguel A. Martinez-del-Amor, Ignacio Perez-Hurtado, Mario J. Perez-Jimenez

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Tags: Biology, Computer science, CUDA, nVidia, P systems, Tesla C1060

February 21, 2011 by hgpu

Enhancing the simulation of P systems for the SAT problem on GPUs

J.M. Cecilia, J.M. Garcia, G.D. Guerrero, M.A. Martinez-Amor, M.J. Perez-Jimenez, M. Ujaldon

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Tags: Biology, CUDA, nVidia, P systems, SAT, Tesla C1060

February 16, 2011 by hgpu

Accelerating the Stochastic Simulation Algorithm using Emerging Architectures

David Dewayne Jenkins

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Tags: Biology, CUDA, Monte Carlo simulation, nVidia, nVidia GeForce 8600 M, Stochastic simulation, Tesla C1060, Tesla C870, Thesis

February 16, 2011 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

Efficient parallel algorithms for maximum-density segment problem

FluoroSim: A Visual Problem-Solving Environment for Fluorescence Microscopy

STOCHSIMGPU: Parallel stochastic simulation for the Systems Biology Toolbox 2 for MATLAB

CUDAlign: using GPU to accelerate the comparison of megabase genomic sequences

Size Matters: Space/Time Tradeoffs to Improve GPGPU Applications Performance

HexServer: an FFT-based protein docking server powered by graphics processors

A Resource-Efficient Computing Paradigm for Computational Protein Modeling Applications

Probing biomolecular machines with graphics processors

Accelerating the Stochastic Simulation Algorithm

A massively parallel framework using P systems and GPUs

Enhancing the simulation of P systems for the SAT problem on GPUs

Accelerating the Stochastic Simulation Algorithm using Emerging Architectures

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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