high performance computing on graphics processing units: hgpu.org

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hgpu.org » Applications » Biology

Parallelizing the cellular potts model on GPU and multi-core CPU: An OpenCL cross-platform study

Chao Yu, Bo Yang

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Tags: ATI, ATI Radeon HD 7870, Biology, Computer science, OpenCL

July 1, 2014 by hgpu

Various String Matching Algorithms for DNA Sequences to Detect Breast Cancer using CUDA Processors

Nagaveni V, G T Raju

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Tags: Algorithms, Bioinformatics, Biology, CUDA, Databases, Medicine, nVidia, String matching, Tesla C2070

June 28, 2014 by hgpu

An efficient parallel algorithm for accelerating computational protein design

Yichao Zhou, Wei Xu, Bruce R. Donald, Jianyang Zeng

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Tags: Algorithms, Bioinformatics, Biology, CUDA, Java, nVidia, Package, Tesla K20

June 23, 2014 by hgpu

Fast Sequence Alignment Method Using CUDA-enabled GPU

Yeim-Kuan Chang, De-Yu Chen

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Tags: Bioinformatics, Biology, CUDA, nVidia, Sequence alignment, Smith-Waterman algorithm, Tesla C1060

June 19, 2014 by hgpu

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

Yilan Liu

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Tags: Bioinformatics, Biology, Computer science, CUDA, Next-Generation sequencing, nVidia, nVidia GeForce GTX 770

June 13, 2014 by hgpu

GPU-Accelerated Dynamic Functional Connectivity Analysis for Functional MRI Data Using OpenCL

D. Akgün, Ü. Sakoğlu, M. Mete, J. Esquivel, B. Adinoff

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Tags: Biology, Magnetic resonance imaging, Medicine, MRI, Neuroscience, nVidia, nVidia GeForce GTX 660, OpenCL

June 9, 2014 by hgpu

Massive exploration of perturbed conditions of the blood coagulation cascade through GPU parallelization

Paolo Cazzaniga, Marco S. Nobile, Daniela Besozzi, Matteo Bellini, Giancarlo Mauri

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Tags: Bioinformatics, Biology, Computational biology, CUDA, Differential equations, nVidia, ODEs, Ordinary differential equations, Tesla K20

May 30, 2014 by hgpu

Performance Evaluation of Quicksort with GPU Dynamic Parallelism for Gene-Expression Quantile Normalization

Roberto Pinto Souto, Carla Osthoff, Douglas Augusto, Oswaldo Trelles, Ana Tereza Ribeiro de Vasconcelos

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Tags: Algorithms, Bioinformatics, Biology, CUDA, nVidia, Sorting, Tesla K20

May 29, 2014 by hgpu

GPU-BSM: A GPU-Based Tool to Map Bisulfite-Treated Reads

Andrea Manconi, Alessandro Orro, Emanuele Manca, Giuliano Armano, Luciano Milanesi

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Tags: Bioinformatics, Biology, CUDA, Genetics, nVidia, nVidia GeForce GTX 480, Package, Python, Sequence alignment, Tesla K10, Tesla K20

May 25, 2014 by hgpu

Graphic Processing Unit Simulation of Axon Growth and Guidance through Cue Diffusion on Massively Parallel Processors

Ana M. Mihut, Graham Morgan, Marcus Kaiser

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Tags: Biology, CUDA, GLSL, Neuroscience, nVidia, nVidia GeForce GTX 460, nVidia Quadro 600, OpenGL, Programming techniques, Tesla K20

May 24, 2014 by hgpu

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

Jing Zhang, Hao Wang, Heshan Lin, Wu-chun Feng

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Tags: Bioinformatics, Biology, CUDA, Next-Generation sequencing, nVidia, Sequence alignment, Tesla K20

May 23, 2014 by hgpu

A performance/cost evaluation for a GPU-based drug discovery application on volunteer computing

Gines David Guerrero Hernandez, Baldomero Imbernon, Horacio Perez-Sanchez, Francisco Sanz, Jose M. Garcia, Jose M. Cecilia

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Tags: Bioinformatics, Biology, CUDA, Medicine, nVidia, nVidia GeForce 7300 GT, nVidia GeForce GTX 465, nVidia GeForce GTX 480, nVidia GeForce GTX 590, Tesla C2070, Tesla K20

May 21, 2014 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

Parallelizing the cellular potts model on GPU and multi-core CPU: An OpenCL cross-platform study

Various String Matching Algorithms for DNA Sequences to Detect Breast Cancer using CUDA Processors

An efficient parallel algorithm for accelerating computational protein design

Fast Sequence Alignment Method Using CUDA-enabled GPU

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

GPU-Accelerated Dynamic Functional Connectivity Analysis for Functional MRI Data Using OpenCL

Massive exploration of perturbed conditions of the blood coagulation cascade through GPU parallelization

Performance Evaluation of Quicksort with GPU Dynamic Parallelism for Gene-Expression Quantile Normalization

GPU-BSM: A GPU-Based Tool to Map Bisulfite-Treated Reads

Graphic Processing Unit Simulation of Axon Growth and Guidance through Cue Diffusion on Massively Parallel Processors

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

A performance/cost evaluation for a GPU-based drug discovery application on volunteer computing

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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