high performance computing on graphics processing units: hgpu.org

Applications

hgpu.org » Applications » Biology

Performance Analysis of IBM Cell Broadband Engine on Sequence Alignment

Yang Song, Gregory M. Striemer, Ali Akoglu

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Tags: Bioinformatics, Biology, Cell processor, CUDA, nVidia, Sequence alignment, Smith-Waterman algorithm, Tesla C870

November 27, 2010 by hgpu

Accelerating leukocyte tracking using CUDA: A case study in leveraging manycore coprocessors

M. Boyer, D. Tarjan, S. T. Acton, K. Skadron

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Tags: Biology, CUDA, Microscopy, nVidia, nVidia GeForce GTX 280

November 26, 2010 by hgpu

Many-core algorithms for statistical phylogenetics

Marc A. Suchard, Andrew Rambaut

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

November 23, 2010 by hgpu

A Parallel Algorithm for Error Correction in High-Throughput Short-Read Data on CUDA-Enabled Graphics Hardware

Haixiang Shi, Bertil Schmidt, Weiguo Liu, Wolfgang Muller-Wittig

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Tags: Biology, Computer science, CUDA, Error recovery, nVidia, Package

November 22, 2010 by hgpu

Parallel Position Weight Matrices Algorithms

Mathieu Giraud, Jean-Stephane Varre

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Tags: Biology, Computer science, CUDA, nVidia, nVidia GeForce 8800, nVidia GeForce GTX 280, Package

November 22, 2010 by hgpu

MSA-CUDA: Multiple Sequence Alignment on Graphics Processing Units with CUDA

Yongchao Liu, Bertil Schmidt, Douglas L. Maskell

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

November 21, 2010 by hgpu

Patient-Specific Non-Linear Finite Element Modelling for Predicting Soft Organ Deformation in Real-Time; Application to Non-Rigid Neuroimage Registration

Adam Wittek, Grand Joldes, Mathieu Couton, Simon K. Warfield, Karol Miller

Tags: Biology, Medicine, nVidia, Surgical simulation, Tesla C870

November 20, 2010 by hgpu

Ultra-fast FFT protein docking on graphics processors

David W. Ritchie, Vishwesh Venkatraman

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Tags: Bioinformatics, Biology, CUDA, FFT, nVidia, nVidia GeForce GTX 285

November 19, 2010 by hgpu

Acceleration of the Smith-Waterman Algorithm using Single and Multiple Graphics Processors

Ali Khajeh-Saeed, Stephen Poole, J. Blair Perot

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Tags: Bioinformatics, Biology, CUDA, nVidia, nVidia GeForce 9800 GT, nVidia GeForce 9800 GTX, nVidia GeForce GTX 295, Sequence matching, Smith-Waterman algorithm

November 18, 2010 by hgpu

GPU-enabled FREALIGN: Accelerating single particle 3D reconstruction and refinement in Fourier space on graphic processors

Xueming Li, Nikolaus Grigorieff, Yifan Cheng

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Tags: Biology, CUDA, Electron microscopy, Image reconstruction, nVidia, Package

November 18, 2010 by hgpu

Low cost, high performance GPU computing solution for atomic resolution cryoEM single-particle reconstruction

Xiaokang Zhang, Xing Zhang, Z. Hong Zhou

Tags: Biology, Cryo-EM, CUDA, Image reconstruction, nVidia

November 18, 2010 by hgpu

An adaptive Expectation-Maximization algorithm with GPU implementation for electron cryomicroscopy

Hemant D. Tagare, Andrew Barthel, Fred J. Sigworth

Tags: Algorithms, Biology, Cryo-EM, CUDA, Image reconstruction, nVidia

November 18, 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 Analysis of IBM Cell Broadband Engine on Sequence Alignment

Accelerating leukocyte tracking using CUDA: A case study in leveraging manycore coprocessors

Many-core algorithms for statistical phylogenetics

A Parallel Algorithm for Error Correction in High-Throughput Short-Read Data on CUDA-Enabled Graphics Hardware

Parallel Position Weight Matrices Algorithms

MSA-CUDA: Multiple Sequence Alignment on Graphics Processing Units with CUDA

Patient-Specific Non-Linear Finite Element Modelling for Predicting Soft Organ Deformation in Real-Time; Application to Non-Rigid Neuroimage Registration

Ultra-fast FFT protein docking on graphics processors

Acceleration of the Smith-Waterman Algorithm using Single and Multiple Graphics Processors

GPU-enabled FREALIGN: Accelerating single particle 3D reconstruction and refinement in Fourier space on graphic processors

Low cost, high performance GPU computing solution for atomic resolution cryoEM single-particle reconstruction

An adaptive Expectation-Maximization algorithm with GPU implementation for electron cryomicroscopy

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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