high performance computing on graphics processing units: hgpu.org

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hgpu.org » Applications » Biology

Fast short exact repeats finding on GPU

Weidong Sun, Weiwei Wang, Zongmin Ma

Tags: Algorithms, Biology, CUDA, Genetics, nVidia, Pattern Search

May 13, 2011 by hgpu

Fast network centrality analysis using GPUs

Zhiao Shi, Bing Zhang

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Tags: All-Pairs Distance, Bioinformatics, Biology, CUDA, nVidia, Package, Tesla C2050

May 13, 2011 by hgpu

Exact and complete short-read alignment to microbial genomes using Graphics Processing Unit programming

Jochen Blom, Tobias Jakobi, Daniel Doppmeier, Sebastian Jaenicke, Jorn Kalinowski, Jens Stoye, Alexander Goesmann

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Tags: Algorithms, Bioinformatics, Biology, CUDA, Next-Generation sequencing, nVidia, Package

May 10, 2011 by hgpu

Fast Parallel Tandem Mass Spectral Library Searching Using GPU Hardware Acceleration

Lydia A. Baumgardner, Avinash K. Shanmugam, Henry Lam, Jimmy K. Eng, Daniel B. Martin

Tags: Biology, Chemistry, CUDA, nVidia, Search, Spectrometry

May 10, 2011 by hgpu

Efficient Parallelization of the Stochastic Simulation Algorithm for Chemically Reacting Systems On the Graphics Processing Unit

Hong Li, Linda Petzold

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Tags: Biology, Chemistry, CUDA, nVidia, nVidia GeForce 8800 GTX, Stochastic simulation

May 10, 2011 by hgpu

A GPU-based architecture for real-time data assessment at synchrotron experiments

Suren Chilingaryan, Alessandro Mirone, Andrew Hammersley,Claudio Ferrero, Lukas Helfen, Andreas Kopmann, Tomy dos Santos Rolo

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Tags: Biology, Image reconstruction, Materials Science, Medicine, nVidia, nVidia GeForce GTX 280, nVidia GeForce GTX 295, nVidia GeForce GTX 480, Poster, Tomography

May 8, 2011 by hgpu

GPU Based Parallel Computing on Blast Program

Huang Lican, Hu Ya

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Tags: Bioinformatics, Biology, BLAST, Sequence alignment

May 7, 2011 by hgpu

GPU acceleration for statistical gene classification

Alfredo Benso, Stefano Di Carlo, Gianfranco Politano, Alessandro Savino

Tags: Bioinformatics, Biology, CUDA, Genetics, nVidia

May 5, 2011 by hgpu

Accelerating scientific applications using GPU’s

M. Taher

Tags: Bioinformatics, Biology, Computer science, CUDA, FFT, nVidia, Security, Sequence alignment

May 3, 2011 by hgpu

Accelerating DNA analysis applications on GPU clusters

A. Tumeo, O. Villa

Tags: Bioinformatics, Biology, GPU cluster, MPI, nVidia, Tesla C1060

April 28, 2011 by hgpu

Parallel Approaches for SWAMP Sequence Alignment

Shannon Steinfadt, Kevin Schaffer

Tags: Bioinformatics, Biology, Cell processor, FPGA, nVidia, Sequence alignment, Smith-Waterman algorithm

April 19, 2011 by hgpu

CUDA-BLASTP: Accelerating BLASTP on CUDA-Enabled Graphics Hardware

Weiguo Liu, Bertil Schmidt, Wolfgang Muller-Wittig

Source codes

Tags: Bioinformatics, Biology, BLAST, CUDA, nVidia, nVidia GeForce GTX 295, Package, Sequence alignment

April 18, 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

Fast short exact repeats finding on GPU

Fast network centrality analysis using GPUs

Exact and complete short-read alignment to microbial genomes using Graphics Processing Unit programming

Fast Parallel Tandem Mass Spectral Library Searching Using GPU Hardware Acceleration

Efficient Parallelization of the Stochastic Simulation Algorithm for Chemically Reacting Systems On the Graphics Processing Unit

A GPU-based architecture for real-time data assessment at synchrotron experiments

GPU Based Parallel Computing on Blast Program

GPU acceleration for statistical gene classification

Accelerating scientific applications using GPU’s

Accelerating DNA analysis applications on GPU clusters

Parallel Approaches for SWAMP Sequence Alignment

CUDA-BLASTP: Accelerating BLASTP on CUDA-Enabled Graphics Hardware

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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