high performance computing on graphics processing units: hgpu.org

Ruibang Luo, Thomas Wong, Jianqiao Zhu, Chi-Man Liu, Edward Wu, Lap-Kei Lee, Haoxiang Lin, Wenjuan Zhu, David W. Cheung, Hing-Fung Ting, Siu-Ming Yiu, Chang Yu, Yingrui Li, Ruiqiang Li, Tak-Wah Lam

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Tags: Algorithms, Bioinformatics, Biology, CUDA, Next-Generation sequencing, nVidia, Package, Tesla C2070, Tesla M2050

February 25, 2013 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

GHOSTM: A GPU-Accelerated Homology Search Tool for Metagenomics

Shuji Suzuki, Takashi Ishida, Ken Kurokawa, Yutaka Akiyama

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Tags: Algorithms, Biology, CUDA, Databases, Next-Generation sequencing, nVidia, Package, Tesla S1070

May 10, 2012 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

Exact and complete short read alignment to microbial genomes using GPU programming

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

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Tags: Bioinformatics, Biology, CUDA, Next-Generation sequencing, nVidia, nVidia GeForce GTX 280, Package

April 11, 2011 by hgpu

DecGPU: distributed error correction on massively parallel graphics processing units using CUDA and MPI

Yongchao Liu, Bertil Schmidt, Douglas Maskell

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Tags: Bioinformatics, Biology, CUDA, MPI, Next-Generation sequencing, nVidia, OpenMP, Package, Tesla S1070

April 11, 2011 by hgpu

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

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

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high performance computing on graphics processing units: hgpu.org

AnySeq/GPU: A Novel Approach for Faster Sequence Alignment on GPUs

eccCL: parallelized GPU implementation of Ensemble Classifier Chains

Parallelization, Scalability, and Reproducibility in Next-Generation Sequencing Analysis

SW#db: GPU-accelerated exact sequence similarity database search

GPU-accelerated Computation for Statistical Analysis of the Next-Generation Sequencing Data

cuBLASTP: Fine-Grained Parallelization of Protein Sequence Search on a GPU

SOAP3-dp: Fast, Accurate and Sensitive GPU-based Short Read Aligner

G-SNPM – A GPU-based SNP mapping tool

GHOSTM: A GPU-Accelerated Homology Search Tool for Metagenomics

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

Exact and complete short read alignment to microbial genomes using GPU programming

DecGPU: distributed error correction on massively parallel graphics processing units using CUDA and MPI

Recent source codes

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

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

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