high performance computing on graphics processing units: hgpu.org

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GPU-RMAP: Accelerating Short-Read Mapping on Graphics Processors

Ashwin M. Aji, Liqing Zhang, Wu C. Feng

Tags: Bioinformatics, Biology, Next-Generation sequencing, nVidia

March 9, 2011 by hgpu

A tile-based parallel Viterbi algorithm for biological sequence alignment on GPU with CUDA

Zhihui Du, Zhaoming Yin, David A. Bader

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Tags: Bioinformatics, Biology, CUDA, nVidia, nVidia GeForce 9800 GTX, Sequence alignment

March 7, 2011 by hgpu

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

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

Graphics Processing Units and Genetic Programming: An overview

W. B. Langdon

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Tags: Bioinformatics, Computer science, CUDA, Genetic programming, nVidia, Review

February 15, 2011 by hgpu

GPU-powered tools boost molecular visualization

Matthieu Chavent, Bruno Levy, Michael Krone, Katrin Bidmon, Jean-Philippe P. Nomine, Thomas Ertl, Marc Baaden

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Tags: Bioinformatics, Biology, Molecular modeling, nVidia, Review, Visualization

February 12, 2011 by hgpu

Supercomputing with toys: harnessing the power of NVIDIA 8800GTX and playstation 3 for bioinformatics problem

Justin Wilson, Manhong Dai, Elvis Jakupovic, Stanley Watson, Fan Meng

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Tags: Bioinformatics, Cell processor, CUDA, nVidia, nVidia GeForce 8800 GTX, Performance, Playstation, RapidMind

January 26, 2011 by hgpu

Evolving GeneChip correlation predictors on parallel graphics hardware

William B. Langdon

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Tags: Bioinformatics, Computer science, Genetic programming, nVidia, nVidia GeForce 8800 GTX, OpenGL, Package, RapidMind

January 21, 2011 by hgpu

Energy efficient biomolecular simulations with FPGA-based reconfigurable computing

Ananth Nallamuthu, Melissa C. Smith, Scott Hampton, Pratul K. Agarwal, Sadaf R. Alam

Tags: Bioinformatics, Biology, FPGA, Molecular dynamics

January 19, 2011 by hgpu

Coccinelle: a C code transformation engine using SmPL for matches, refactorings, and bug fixing

Advances in Semantic Patching for HPC-oriented Refactorings with Coccinelle

DuoReduce: MLIR's benchmark

Hardware-Assisted Software Testing and Debugging for Heterogeneous Computing

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

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high performance computing on graphics processing units: hgpu.org

GPU-RMAP: Accelerating Short-Read Mapping on Graphics Processors

A tile-based parallel Viterbi algorithm for biological sequence alignment on GPU with CUDA

Efficient parallel algorithms for maximum-density segment problem

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

Graphics Processing Units and Genetic Programming: An overview

GPU-powered tools boost molecular visualization

Supercomputing with toys: harnessing the power of NVIDIA 8800GTX and playstation 3 for bioinformatics problem

Evolving GeneChip correlation predictors on parallel graphics hardware

Energy efficient biomolecular simulations with FPGA-based reconfigurable computing

Recent source codes

Coccinelle: a C code transformation engine using SmPL for matches, refactorings, and bug fixing

DuoReduce: MLIR's benchmark

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

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