high performance computing on graphics processing units: hgpu.org

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hgpu.org » Applications » Biology

Computational modeling of synthetic microbial biofilms

Timothy J Rudge, Paul J Steiner, Andrew Phillips, Jim Haseloff

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Tags: Biology, Biophysics, nVidia, nVidia Quadro FX 5800, OpenCL, Pharmaceuticals

July 28, 2012 by hgpu

Parallelization of Data Intensive Code Using Computer Unified Device Architecture (CUDA)

Bhardwaj Aditi, Bhardwaj Rohatash K., Shishir K. Gangwar

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Tags: Algorithms, Biology, CUDA, nVidia, RNA

July 26, 2012 by hgpu

Parallel-META: efficient metagenomic data analysis based on high-performance computation

Xiaoquan Su, Jian Xu, Kang Ning

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Tags: Biology, Computational biology, CUDA, nVidia, Package, Tesla C2070

July 22, 2012 by hgpu

A Performance Model for Memory Bandwidth Constrained Applications on Graphics Engines

Lin Ma, Roger D. Chamberlain

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Tags: Biology, BLAST, Computational biology, CUDA, Hashing, nVidia, nVidia GeForce GTX 480, Performance

July 15, 2012 by hgpu

GPU-Optimized Molecular Dynamics Simulations

Tyson J. Lipscomb

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Tags: Biology, Biomolecules, CUDA, Molecular dynamics, nVidia, nVidia GeForce GTX 480, nVidia GeForce GTX 580, Optimization, Pseudo-random number generators, Review, RNA, Tesla C2070, Thesis

July 8, 2012 by hgpu

Accelerating large-scale protein structure alignments with graphics processing units

Bin Pang, Nan Zhao, Michela Becchi, Dmitry Korkin, Chi-Ren Shyu

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Tags: Bioinformatics, Biology, CUDA, Java, nVidia, Package, Tesla C2050

June 30, 2012 by hgpu

GPU-based Cloud Computing for Comparing the Structure of Protein Binding Sites

Matthias Leinweber, Lars Baumgartner, Marco Mernberger, Thomas Fober, Eyke Hullermeier, Gerhard Klebe, Bernd Freisleben

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Tags: Biology, Java, Macromolecule, nVidia, nVidia GeForce GTX 580, OpenCL, Tesla M2050

June 26, 2012 by hgpu

CUSHAW: a CUDA compatible short read aligner to large genomes based on the Burrows-Wheeler transform

Yongchao Liu, Bertil Schmidt, Douglas L. Maskell

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Tags: Bioinformatics, Biology, CUDA, nVidia, Package, Tesla C2050

June 21, 2012 by hgpu

Parallel Implementation of the Wu-Manber Algorithm Using the OpenCL Framework

Themistoklis K. Pyrgiotis, Charalampos S. Kouzinopoulos, Konstantinos G. Margaritis

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Tags: Algorithms, Biology, Computational biology, Databases, nVidia, nVidia GeForce GTX 280, OpenCL, Pattern Search, Sequence matching

June 20, 2012 by hgpu

GPUmotif: An Ultra-Fast and Energy-Efficient Motif Analysis Program Using Graphics Processing Units

Pooya Zandevakili, Ming Hu, Zhaohui Qin

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Tags: Algorithms, Biochemistry, Biology, Chemistry, Computational biology, Computer science, CUDA, Genetics, nVidia, nVidia GeForce GTX 260, nVidia GeForce GTX 480, Package

June 17, 2012 by hgpu

Range query processing in a multi-GPU environment

Ricardo J. Barrientos, Jose I. Gomez, Christian Tenllado, Manuel Prieto Matias, Mauricio Marin

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Tags: Algorithms, Biology, Computational biology, Computer science, CUDA, Databases, GPU cluster, nVidia, OpenMP, Tesla C1060

June 11, 2012 by hgpu

CUDAICA: GPU optimization of Infomax-ICA EEG analysis

Federico Raimondo, Juan Kamienkowski, Mariano Sigman, Diego Fernandez Slezak

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Tags: Algorithms, Biology, CUBLAS, CUDA, Linear Algebra, Matrix multiplication, Neuroscience, nVidia, nVidia GeForce GTX 560, Package, Tesla C2070

June 11, 2012 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

Computational modeling of synthetic microbial biofilms

Parallelization of Data Intensive Code Using Computer Unified Device Architecture (CUDA)

Parallel-META: efficient metagenomic data analysis based on high-performance computation

A Performance Model for Memory Bandwidth Constrained Applications on Graphics Engines

GPU-Optimized Molecular Dynamics Simulations

Accelerating large-scale protein structure alignments with graphics processing units

GPU-based Cloud Computing for Comparing the Structure of Protein Binding Sites

CUSHAW: a CUDA compatible short read aligner to large genomes based on the Burrows-Wheeler transform

Parallel Implementation of the Wu-Manber Algorithm Using the OpenCL Framework

GPUmotif: An Ultra-Fast and Energy-Efficient Motif Analysis Program Using Graphics Processing Units

Range query processing in a multi-GPU environment

CUDAICA: GPU optimization of Infomax-ICA EEG analysis

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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