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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

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

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

Compute Distance Matrices with GPU

Seongho Kim, Ming Ouyang

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Tags: Bioinformatics, Biology, Computer science, CUDA, nVidia, Tesla C2050

October 1, 2012 by hgpu

Speeding up Scoring Module of Mass Spectrometry Based Protein Identification by GPU

You Li, Xiaowen Chu

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Tags: Bioinformatics, Biology, CUDA, Databases, nVidia, nVidia GeForce GTX 280, Spectrometry

September 25, 2012 by hgpu

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

CUDA-L2: Surpassing cuBLAS Performance for Matrix Multiplication through Reinforcement Learning

BoltzGen:Toward Universal Binder Design

cuPilot: A Strategy-Coordinated Multi-agent Framework for CUDA Kernel Evolution

MATLAB Tensor Core models

Accurate Models of NVIDIA Tensor Cores

TritonForge: Transform PyTorch Operations into Optimized GPU Kernels with LLMs

TritonForge: Profiling-Guided Framework for Automated Triton Kernel Optimization

RLTune: Hybrid Learning and Optimization-Based Dynamic Scheduling for DL Workloads on Heterogeneous GPU Clusters

Hybrid Learning and Optimization-Based Dynamic Scheduling for DL Workloads on Heterogeneous GPU Clusters

tritonBLAS: A Lightweight Triton-based General Matrix Multiplication (GEMM) Library

tritonBLAS: Triton-based Analytical Approach for GEMM Kernel Parameter Selection

See all packages

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high performance computing on graphics processing units: hgpu.org

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

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

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

Compute Distance Matrices with GPU

Speeding up Scoring Module of Mass Spectrometry Based Protein Identification by GPU

Recent source codes

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

CUDA-L2: Surpassing cuBLAS Performance for Matrix Multiplication through Reinforcement Learning

BoltzGen:Toward Universal Binder Design

cuPilot: A Strategy-Coordinated Multi-agent Framework for CUDA Kernel Evolution

MATLAB Tensor Core models

TritonForge: Transform PyTorch Operations into Optimized GPU Kernels with LLMs

RLTune: Hybrid Learning and Optimization-Based Dynamic Scheduling for DL Workloads on Heterogeneous GPU Clusters

tritonBLAS: A Lightweight Triton-based General Matrix Multiplication (GEMM) Library

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