high performance computing on graphics processing units: hgpu.org

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hgpu.org » Applications » Biology

Multifactor dimensionality reduction for graphics processing units enables genome-wide testing of epistasis in sporadic ALS

Casey S. Greene, Nicholas A. Sinnott-Armstrong, Daniel S. Himmelstein, Paul J. Park, Jason H. Moore, Brent T. Harris

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Tags: Bioinformatics, Biology, CUDA, Genetics, nVidia, nVidia GeForce GTX 295, Package

November 7, 2010 by hgpu

Performance Analysis of General-Purpose Computation on Commodity Graphics Hardware: A Case Study Using Bioinformatics

Weiguo Liu, Bertil Schmidt, Wolfgang Muller-Wittig

Tags: Biology, Computer science, nVidia, Sequence alignment, Signal processing

November 7, 2010 by hgpu

Accelerating epistasis analysis in human genetics with consumer graphics hardware

Nicholas S. Armstrong, Casey Greene, Fabio Cancare, Jason Moore

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Tags: Bioinformatics, Biology, CUDA, Genetics, nVidia, nVidia GeForce GTX 280

November 7, 2010 by hgpu

CUDASW++ 2.0: enhanced Smith-Waterman protein database search on CUDA-enabled GPUs based on SIMT and virtualized SIMD abstractions

Yongchao Liu, Bertil Schmidt, Douglas Maskell

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Tags: Bioinformatics, Biology, Computational biology, CUDA, nVidia, nVidia GeForce GTX 280, nVidia GeForce GTX 295, Package, Smith-Waterman algorithm

November 6, 2010 by hgpu

Automatic fitting of spiking neuron models to electrophysiological recordings

Cyrille Rossant, Dan F. Goodman, Jonathan Platkiewicz, Romain Brette

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Tags: Adaptive threshold, Biology, CUDA, Distributed computing, Neuroscience, nVidia, nVidia GeForce GTX 295, Optimization, Package

November 6, 2010 by hgpu

A matrix approach to tomographic reconstruction and its implementation on GPUs

F. Vazquez, E. M. Garzon, J. J. Fernandez

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Tags: Biology, Image processing, Sparse matrix

November 6, 2010 by hgpu

Efficient simulation of large-scale spiking neural networks using CUDA graphics processors

Jayram M. Nageswaran, Nikil Dutt, Jeffrey L. Krichmar, Alex Nicolau, Alex Veidenbaum

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Tags: Biology, Computer science, CUDA, Neural networks, nVidia, nVidia GeForce GTX 280, STDP

November 6, 2010 by hgpu

CUDASW++: optimizing Smith-Waterman sequence database searches for CUDA-enabled graphics processing units

Yongchao Liu, Douglas Maskell, Bertil Schmidt

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Tags: Bioinformatics, Biology, Computational biology, CUDA, nVidia, nVidia GeForce GTX 280, nVidia GeForce GTX 295, Package, Smith-Waterman algorithm

November 4, 2010 by hgpu

Molecular Simulation of ab Initio Protein Folding for a Millisecond Folder NTL9(1-39)

Vincent A. Voelz, Gregory R. Bowman, Kyle Beauchamp, Vijay S. Pande

Tags: Bioinformatics, Biology, Chemistry, Molecular dynamics

November 4, 2010 by hgpu

Streaming Algorithms for Biological Sequence Alignment on GPUs

Weiguo Liu, Bertil Schmidt, Gerrit Voss, Wolfgang M. Wittig

Tags: Biology, Sequence alignment

November 3, 2010 by hgpu

Fast and accurate protein substructure searching with simulated annealing and GPUs

Alex D. Stivala, Peter J. Stuckey, Anthony I. Wirth

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Tags: Bioinformatics, Biological Physics, Biology, CUDA, Molecular dynamics, nVidia, nVidia GeForce GTX 285, Package, Tesla C1060

November 2, 2010 by hgpu

GPU-ClustalW: Using Graphics Hardware to Accelerate Multiple Sequence Alignment

Weiguo Liu, Bertil Schmidt, Gerrit Voss, Wolfgang Müller-Wittig

Tags: Bioinformatics, Biology, Computational biology, Computer science, Sequence alignment

November 1, 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

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high performance computing on graphics processing units: hgpu.org

Applications

Multifactor dimensionality reduction for graphics processing units enables genome-wide testing of epistasis in sporadic ALS

Performance Analysis of General-Purpose Computation on Commodity Graphics Hardware: A Case Study Using Bioinformatics

Accelerating epistasis analysis in human genetics with consumer graphics hardware

CUDASW++ 2.0: enhanced Smith-Waterman protein database search on CUDA-enabled GPUs based on SIMT and virtualized SIMD abstractions

Automatic fitting of spiking neuron models to electrophysiological recordings

A matrix approach to tomographic reconstruction and its implementation on GPUs

Efficient simulation of large-scale spiking neural networks using CUDA graphics processors

CUDASW++: optimizing Smith-Waterman sequence database searches for CUDA-enabled graphics processing units

Molecular Simulation of ab Initio Protein Folding for a Millisecond Folder NTL9(1-39)

Streaming Algorithms for Biological Sequence Alignment on GPUs

Fast and accurate protein substructure searching with simulated annealing and GPUs

GPU-ClustalW: Using Graphics Hardware to Accelerate Multiple Sequence Alignment

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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