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Accelerated Large-Scale Multiple Sequence Alignment

Scott Lloyd, Quinn O. Snell

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Tags: Algorithms, Bioinformatics, Biology, FPGA, Package, Sequence alignment

January 19, 2012 by hgpu

BarraCUDA – a fast short read sequence aligner using graphics processing units

Petr Klus, Simon Lam, Dag Lyberg, Ming Sin Cheung, Graham Pullan, Ian McFarlane, Giles S. H. Yeo, Brian Y. H. Lam

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Tags: Bioinformatics, Biology, CUDA, nVidia, Package, Sequence alignment, Tesla M2050, Tesla M2090

January 13, 2012 by hgpu

Parallel mutual information estimation for inferring gene regulatory networks on GPUs

Haixiang Shi, Bertil Schmidt, Weiguo Liu, Wolfgang Muller-Wittig

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Tags: Algorithms, Biology, Computational biology, CUDA, Image processing, Machine learning, nVidia, Package, Tesla C2050

January 13, 2012 by hgpu

MetaBinG: Using GPUs to Accelerate Metagenomic Sequence Classification

Peng Jia, Liming Xuan, Lei Liu, Chaochun Wei

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Tags: Biology, Computational biology, CUDA, Genetics, nVidia, Package, Tesla C1060

January 11, 2012 by hgpu

Building Human Brain Network in 3D Coefficient Map Determined by X-ray Microtomography

Ryuta Mizutani, Akihisa Takeuchi, Kentaro Uesugi, Susumu Takekoshi, Naoya Nakamura, Yoshio Suzuki

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Tags: Biology, CUDA, Image reconstruction, Medicine, nVidia, nVidia GeForce GTX 470, Package, Tomography

December 30, 2011 by hgpu

An Efficient Simulation Environment for Modeling Large-Scale Cortical Processing

Micah Richert, Jayram Moorkanikara Nageswaran, Nikil Dutt, Jeffrey L. Krichmar

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Tags: Biology, CUDA, Neural networks, Neuroscience, nVidia, Package, Tesla C1060

December 19, 2011 by hgpu

On the design of architecture-aware algorithms for emerging applications

Seunghwa Kang

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Tags: Algorithms, Benchmarking, Biology, Cell processor, Computational biology, CUDA, Image processing, MapReduce, nVidia, Package, Tesla C1060, Thesis

December 2, 2011 by hgpu

Application of GPGPU for Acceleration of Short DNA Sequence Alignment in Unipro UGENE Project

Konstantin Okonechinkov, German Grekhov, Konstantin Stepanyuk, Mikhail Fursov

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Tags: Algorithms, Bioinformatics, Biology, nVidia, OpenCL, Package, Sequence alignment, Tesla C1060, Tesla C2070

November 22, 2011 by hgpu

An Ultrafast Scalable Many-core Motif Discovery Algorithm for Multiple GPUs

Yongchao Liu, Bertil Schmidt, Douglas L. Maskell

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Tags: Algorithms, Benchmarking, Biology, CUDA, GPU cluster, MPI, nVidia, OpenMP, Package, Tesla S2050

November 15, 2011 by hgpu

GSNP: A DNA Single-Nucleotide Polymorphism Detection System with GPU Acceleration

Mian Lu, Jiuxin Zhao, Qiong Luo, Bingqiang Wang, Shaohua Fu, Zhe Lin

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Tags: Bioinformatics, Biology, Compression, nVidia, Package, Sorting, Tesla M2050

November 12, 2011 by hgpu

DOPA: GPU-based protein alignment using database and memory access optimizations

Laiq Hasan, Marijn Kentie, Zaid Al-Ars

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Tags: Algorithms, Bioinformatics, Biology, Computational Complexity, CUDA, Databases, nVidia, nVidia GeForce GTX 275, Optimization, Package, Sequence alignment, Smith-Waterman algorithm

October 21, 2011 by hgpu

Democratic Population Decisions Result in Robust Policy-Gradient Learning: A Parametric Study with GPU Simulations

Paul Richmond, Lars Buesing, Michele Giugliano, Eleni Vasilaki

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Tags: Biology, CUDA, Neuroscience, nVidia, nVidia GeForce GTX 480, Package, Python

October 5, 2011 by hgpu

HPCTransCompile: An AI Compiler Generated Dataset for High-Performance CUDA Transpilation and LLM Preliminary Exploration

Efficient Graph Embedding at Scale: Optimizing CPU-GPU-SSD Integration

Can Large Language Models Predict Parallel Code Performance?

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high performance computing on graphics processing units: hgpu.org

Packages

Accelerated Large-Scale Multiple Sequence Alignment

BarraCUDA – a fast short read sequence aligner using graphics processing units

Parallel mutual information estimation for inferring gene regulatory networks on GPUs

MetaBinG: Using GPUs to Accelerate Metagenomic Sequence Classification

Building Human Brain Network in 3D Coefficient Map Determined by X-ray Microtomography

An Efficient Simulation Environment for Modeling Large-Scale Cortical Processing

On the design of architecture-aware algorithms for emerging applications

Application of GPGPU for Acceleration of Short DNA Sequence Alignment in Unipro UGENE Project

An Ultrafast Scalable Many-core Motif Discovery Algorithm for Multiple GPUs

GSNP: A DNA Single-Nucleotide Polymorphism Detection System with GPU Acceleration

DOPA: GPU-based protein alignment using database and memory access optimizations

Democratic Population Decisions Result in Robust Policy-Gradient Learning: A Parametric Study with GPU Simulations

Recent source codes

HPCTransCompile: An AI Compiler Generated Dataset for High-Performance CUDA Transpilation and LLM Preliminary Exploration

chemtrain: Training Molecular Dynamics Potentials in JAX

microSYCL: SYCL micro-benchmarks repository

XaaS containers

SYCL Container

CASS: Cuda-Amd aSSembly

Cluser of smartphones for edge computing application using TensorFlow

CFAL-bench

Efficient Graph Embedding at Scale: Optimizing CPU-GPU-SSD Integration

Can Large Language Models Predict Parallel Code Performance?

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