high performance computing on graphics processing units: hgpu.org

Applications

hgpu.org » Applications » Biology

Burrows-Wheeler Aligner: A Parallel Approach

Sheridan Lee Wright

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Tags: Algorithms, Bioinformatics, Biology, CUDA, MPI, nVidia, Sequence alignment, Thesis

January 16, 2013 by hgpu

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

True 4-Bit Quantized CNN Training on CPU

True 4-Bit Quantized Convolutional Neural Network Training on CPU: Achieving Full-Precision Parity

cuFuzz: A GPU-oriented coverage-guided fuzzer for userland CUDA application

Hunting CUDA Bugs at Scale with cuFuzz

KernelSkill: A Multi-Agent Framework for GPU Kernel Optimization

MSKernelBench & CUDAMaster

Making LLMs Optimize Multi-Scenario CUDA Kernels Like Experts

EvoScientist: Harness Vibe Research with Self-evolving AI Scientists

EvoScientist: Towards Multi-Agent Evolving AI Scientists for End-to-End Scientific Discovery

RepoLaunch: Automating Build and Test Pipeline of Code Repositories on ANY Language and ANY Platform

RepoLaunch: Automating Build & Test Pipeline of Code Repositories on ANY Language and ANY Platform

RepoLaunch: Automating Build and Test Pipeline of Code Repositories on ANY Language and ANY Platform

RepoLaunch: Automating Build & Test Pipeline of Code Repositories on ANY Language and ANY Platform

CONCUR: a benchmark designed to evaluate multithreaded Java code generated by LLMs

CONCUR: Benchmarking LLMs for Concurrent Code Generation

HIPRT: Ray Tracing using HIP

Ray Tracing using HIP

MXFP4 Training Support Codebase

Practical FP4 Training for Large-Scale MoE Models on Hopper GPUs

See all packages

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high performance computing on graphics processing units: hgpu.org

Applications

Burrows-Wheeler Aligner: A Parallel Approach

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

Recent source codes

True 4-Bit Quantized CNN Training on CPU

cuFuzz: A GPU-oriented coverage-guided fuzzer for userland CUDA application

KernelSkill: A Multi-Agent Framework for GPU Kernel Optimization

MSKernelBench & CUDAMaster

EvoScientist: Harness Vibe Research with Self-evolving AI Scientists

RepoLaunch: Automating Build and Test Pipeline of Code Repositories on ANY Language and ANY Platform

RepoLaunch: Automating Build and Test Pipeline of Code Repositories on ANY Language and ANY Platform

CONCUR: a benchmark designed to evaluate multithreaded Java code generated by LLMs

HIPRT: Ray Tracing using HIP

MXFP4 Training Support Codebase

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