high performance computing on graphics processing units: hgpu.org

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Accelerating molecular docking and binding site mapping using FPGAs and GPUs

Bharat Sukhwani

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Tags: Algorithms, Biology, Biomechanics, CUDA, FPGA, Molecular modeling, nVidia, Tesla C1060, Thesis

October 22, 2011 by hgpu

DOPA: GPU-based protein alignment using database and memory access optimizations

Laiq Hasan, Marijn Kentie, Zaid Al-Ars

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Tags: Algorithms, Bioinformatics, Biology, Computational Complexity, CUDA, Databases, nVidia, nVidia GeForce GTX 275, Optimization, Package, Sequence alignment, Smith-Waterman algorithm

October 21, 2011 by hgpu

Heterogeneous Accelerated Bioinformatics-Perspectives for Cancer Research

Eric A. Stahlberg, T. Steinke, M. C. Smith, S. Chandrasekaran, B. Chapman

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Tags: Bioinformatics, Biology, CUDA, FPGA, Heterogeneous systems, Medicine, nVidia, OpenCL, Review

October 19, 2011 by hgpu

PlinkGPU: A Framework for GPU Acceleration of Whole Genome Data Analysis

Jeffrey Poznanovic

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Tags: Bioinformatics, Biology, CUDA, Genetics, nVidia, OpenCL, Tesla S1070

October 13, 2011 by hgpu

Performance improvements for iterative electron tomography reconstruction using graphics processing units (GPUs)

W.J. Palenstijna, K.J. Batenburga, J. Sijbersa

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Tags: Biology, Image reconstruction, Medicine, nVidia GeForce GTX 280, nVidia GeForce GTX 480, Tomography

October 8, 2011 by hgpu

GPGPU-assisted prediction of ion binding sites in proteins

Leonid Uroshlev, Sergei Rahmanov, Ivan Kulakovskiy, Vsevolod Makeev

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Tags: Biology, Biophysics, CUDA, Molecular modeling, nVidia

October 7, 2011 by hgpu

Democratic Population Decisions Result in Robust Policy-Gradient Learning: A Parametric Study with GPU Simulations

Paul Richmond, Lars Buesing, Michele Giugliano, Eleni Vasilaki

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Tags: Biology, CUDA, Neuroscience, nVidia, nVidia GeForce GTX 480, Package, Python

October 5, 2011 by hgpu

GPU-Accelerated DNA Distance Matrix Computation

Zhi Ying, Xinhua Lin, Simon Chong-Wee See, Minglu Li

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Tags: ATI, ATI Radeon HD 5850, Bioinformatics, Biology, Genetics, nVidia, OpenCL, Performance, Tesla C2050

October 3, 2011 by hgpu

Large Scale DNA Sequence Alignment and Kernel Method Implemented with GPUs

Songwen Pei, Wenhao Wang, Gang Wei, Baifeng Wu

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Tags: Algorithms, ATI, ATI Radeon HD 4870, Bioinformatics, Biology, Brook, Sequence alignment

October 1, 2011 by hgpu

Manycore high-performance computing in bioinformatics

Jean-Stephane Varre, Bertil Schmidt, Stephane Janot, Mathieu Giraud

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Tags: Algorithms, Bioinformatics, Biology, CUDA, nVidia, OpenCL, Review, RNA, Sequence alignment

September 26, 2011 by hgpu

Accelerating reaction-diffusion simulations with general-purpose graphics processing units

Matthias Vigelius, Aidan Lane, Bernd Meyer

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Tags: Algorithms, Bioinformatics, Biology, CUDA, nVidia, Package, Rendering, Stochastic simulation

September 23, 2011 by hgpu

GPU Computation in Bioinspired Algorithms: A Review

M. G. Arenas, A. M. Mora, G. Romero and P. A. Castillo

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Tags: Algorithms, ATI, Bioinformatics, Biology, Computational biology, CUDA, nVidia, OpenCL, Overview, Review

September 8, 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

Accelerating molecular docking and binding site mapping using FPGAs and GPUs

DOPA: GPU-based protein alignment using database and memory access optimizations

Heterogeneous Accelerated Bioinformatics-Perspectives for Cancer Research

PlinkGPU: A Framework for GPU Acceleration of Whole Genome Data Analysis

Performance improvements for iterative electron tomography reconstruction using graphics processing units (GPUs)

GPGPU-assisted prediction of ion binding sites in proteins

Democratic Population Decisions Result in Robust Policy-Gradient Learning: A Parametric Study with GPU Simulations

GPU-Accelerated DNA Distance Matrix Computation

Large Scale DNA Sequence Alignment and Kernel Method Implemented with GPUs

Manycore high-performance computing in bioinformatics

Accelerating reaction-diffusion simulations with general-purpose graphics processing units

GPU Computation in Bioinspired Algorithms: A Review

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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