high performance computing on graphics processing units: hgpu.org

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hgpu.org » Applications » Biology

Acceleration of Selective Cationic Antibacterial Peptides computation: A comparison of FPGA and GPU approaches

D. Garcia-Ordaz, M. Arias-Estrada, M. Nuno-Maganda, C. Polanco, G. Del Rio

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Tags: Bioinformatics, Biology, CUDA, FPGA, nVidia, nVidia GeForce GT 230 M, nVidia GeForce GTX 480, Tesla M2070

January 13, 2013 by hgpu

Optimizations in Bioinformatics using GPU Processing on Binary Data

Manuel Belmadani

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

January 8, 2013 by hgpu

GPU-Optimized Coarse-Grained MD Simulations of Protein and RNA Folding and Assembly

Andrew J. Proctor, Tyson J. Lipscomb, Anqi Zou, Joshua A. Anderson, Samuel S. Cho

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Tags: Bioinformatics, Biology, CUDA, Macromolecule, Molecular dynamics, nVidia, RNA, Tesla C2070

January 8, 2013 by hgpu

Long Timestep Molecular Dynamics on the Graphical Processing Unit

James C. Sweet, Ronald J. Nowling, Trevor Cickovski, Christopher R. Sweet, Vijay S. Pande, Jesus A. Izaguirre

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Tags: Biology, Chemistry, CUDA, Molecular dynamics, nVidia, nVidia GeForce GTX 580, OpenCL, Package

January 4, 2013 by hgpu

High performance bioinformatics and computational biology on general-purpose graphics processing units

Cheng Ling

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Tags: Bioinformatics, Biology, Computational biology, CUDA, FPGA, nVidia, nVidia GeForce 8800 GTX, nVidia GeForce GTX 460, Sequence alignment, Thesis

January 3, 2013 by hgpu

Radionuclides migration modelling using artificial neural networks and parallel computing

O.S. Hilko, S.P. Kundas, I.A. Gishkeluk

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Tags: Algorithms, Biology, CUDA, MPI, Neural networks, nVidia, nVidia GeForce 9500 GT, nVidia GeForce 9800 GT, nVidia GeForce GT 220 M

December 29, 2012 by hgpu

Bioinformatics Sequence Comparisons on Manycore Processors

Tuan Tu Tran

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Tags: ATI, ATI Radeon HD 5870, Bioinformatics, Biology, nVidia, nVidia GeForce GTX 480, OpenCL, Review, Sequence matching, Thesis

December 25, 2012 by hgpu

Efficient reconstruction of biological networks via transitive reduction on general purpose graphics processors

Dragan Bosnacki, Maximilian R Odenbrett, Anton Wijs, Willem Ligtenberg, Peter Hilbers

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Tags: Algorithms, Bioinformatics, Biology, CUDA, nVidia, nVidia GeForce GTX 480, Package

November 23, 2012 by hgpu

G-SNPM – A GPU-based SNP mapping tool

Alessandro Orro, Andrea Manconi, Emanuele Manca, Giuliano Armano, Luciano Milanesi

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Tags: Algorithms, Bioinformatics, Biology, CUDA, Next-Generation sequencing, nVidia, nVidia GeForce GTX 480, Package, Python, Smith-Waterman algorithm

November 14, 2012 by hgpu

GPU Acceleration of Pyrosequencing Noise Removal

Yang Gao, Jason D. Bakos

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Tags: Algorithms, Bioinformatics, Biology, Clustering, CUDA, MPI, nVidia, Sequence alignment, Tesla C2070

November 10, 2012 by hgpu

Quantum.Ligand.Dock: protein-ligand docking with quantum entanglement refinement on a GPU system

Alexander A. Kantardjiev

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Tags: Algorithms, Bioinformatics, Biology, OpenCL, Visualization

November 1, 2012 by hgpu

Accelerated protein structure comparison using TM-score-GPU

Ling-Hong Hung, Ram Samudrala

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Tags: ATI, ATI Radeon HD 5870, Bioinformatics, Biology, Clustering, OpenCL, Package

October 5, 2012 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

Acceleration of Selective Cationic Antibacterial Peptides computation: A comparison of FPGA and GPU approaches

Optimizations in Bioinformatics using GPU Processing on Binary Data

GPU-Optimized Coarse-Grained MD Simulations of Protein and RNA Folding and Assembly

Long Timestep Molecular Dynamics on the Graphical Processing Unit

High performance bioinformatics and computational biology on general-purpose graphics processing units

Radionuclides migration modelling using artificial neural networks and parallel computing

Bioinformatics Sequence Comparisons on Manycore Processors

Efficient reconstruction of biological networks via transitive reduction on general purpose graphics processors

G-SNPM – A GPU-based SNP mapping tool

GPU Acceleration of Pyrosequencing Noise Removal

Quantum.Ligand.Dock: protein-ligand docking with quantum entanglement refinement on a GPU system

Accelerated protein structure comparison using TM-score-GPU

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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