high performance computing on graphics processing units: hgpu.org

hgpu.org » Biology

G-SNPM – A GPU-based SNP mapping tool

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

View

Download (PDF)

Source codes

Tags: Algorithms, Bioinformatics, Biology, CUDA, Next-Generation sequencing, nVidia, nVidia GeForce GTX 480, Package, Python, Smith-Waterman algorithm

November 14, 2012 by hgpu

GPU Acceleration of Pyrosequencing Noise Removal

Yang Gao, Jason D. Bakos

View

Download (PDF)

Tags: Algorithms, Bioinformatics, Biology, Clustering, CUDA, MPI, nVidia, Sequence alignment, Tesla C2070

November 10, 2012 by hgpu

Quantum.Ligand.Dock: protein-ligand docking with quantum entanglement refinement on a GPU system

Alexander A. Kantardjiev

View

Download (PDF)

Tags: Algorithms, Bioinformatics, Biology, OpenCL, Visualization

November 1, 2012 by hgpu

Accelerated protein structure comparison using TM-score-GPU

Ling-Hong Hung, Ram Samudrala

View

Download (PDF)

Source codes

Tags: ATI, ATI Radeon HD 5870, Bioinformatics, Biology, Clustering, OpenCL, Package

October 5, 2012 by hgpu

Compute Distance Matrices with GPU

Seongho Kim, Ming Ouyang

View

Download (PDF)

Tags: Bioinformatics, Biology, Computer science, CUDA, nVidia, Tesla C2050

October 1, 2012 by hgpu

ARVO-CL: The OpenCL version of the ARVO package – An efficient tool for computing the accessible surface area and the excluded volume of proteins via analytical equations

Jan Busa Jr., Shura Hayryan, Ming-Chya Wu, Jan Busa, Chin-Kun Hu

View

Download (PDF)

Tags: Algorithms, Biology, Computer science, nVidia, nVidia GeForce GTX 480, OpenCL

September 30, 2012 by hgpu

Speeding up Scoring Module of Mass Spectrometry Based Protein Identification by GPU

You Li, Xiaowen Chu

View

Download (PDF)

Tags: Bioinformatics, Biology, CUDA, Databases, nVidia, nVidia GeForce GTX 280, Spectrometry

September 25, 2012 by hgpu

Massive parallelization of combinatorial statistical genetics analyses porting machine learning methods on general purpose graphics processing units (GPU)

Tony Kam-Thong

View

Download (PDF)

Source codes

Tags: Biology, CUDA, Genetics, Machine learning, nVidia, nVidia GeForce GTX 295, nVidia GeForce GTX 580, Package, Thesis

September 16, 2012 by hgpu

Accelerating the Smith-Waterman Algorithm for Bio-sequence Matching on GPU

Qianghua Zhu, Fei Xia, Guoqing Jin

View

Download (PDF)

Tags: Algorithms, Bioinformatics, Biology, CUDA, Databases, nVidia, nVidia GeForce GTX 470, Sequence alignment, Sequence matching, Smith-Waterman algorithm

September 16, 2012 by hgpu

High-Throughput parallel blind Virtual Screening using BINDSURF

Irene Sanchez-Linares, Horacio Perez-Sanchez, Jose M Cecilia, Jose M Garcia

View

Download (PDF)

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

September 15, 2012 by hgpu

Hotspot Analysis Based Partial CUDA Acceleration of HMMER 3.0 on GPGPUs

Fahian Ahmed, Saddam Quirem, Gak Min, Byeong Kil Lee

View

Download (PDF)

Tags: Bioinformatics, Biology, CUDA, nVidia, nVidia GeForce GTX 460, Tesla C1060

September 12, 2012 by hgpu

GPU accelerated QTL detection

G. Chapuis, O. Filangi, J.M. Elsen, D. Lavenier, P. Le Roy

View

Download (PDF)

Source codes

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

September 11, 2012 by hgpu

Over-synchronization in GPU Programs

profile_util: simple C++ library to report memory, timing, thread affinity

Profile Util library: A quick and easy way to get MPI, OpenMP and GPU runtime information

MaC: Mamba CPU performance predictor

MambaCPU: Enhanced Correlation Mining with State Space Models for CPU Performance Prediction

Mixed-precision finite element kernels

Mixed-precision finite element kernels and assembly: Rounding error analysis and hardware acceleration

SHMT: The Simultaneous and Heterogenous Multithreading project

General-Purpose Computing on Tensor Processors

Superpipeline: A Universal Approach for Reducing GPU Memory Usage in Large Models

EnergyUCB-Bandit

Online Energy Optimization in GPUs: A Multi-Armed Bandit Approach

See all packages

* * *

high performance computing on graphics processing units: hgpu.org

G-SNPM – A GPU-based SNP mapping tool

GPU Acceleration of Pyrosequencing Noise Removal

Quantum.Ligand.Dock: protein-ligand docking with quantum entanglement refinement on a GPU system

Accelerated protein structure comparison using TM-score-GPU

Compute Distance Matrices with GPU

ARVO-CL: The OpenCL version of the ARVO package – An efficient tool for computing the accessible surface area and the excluded volume of proteins via analytical equations

Speeding up Scoring Module of Mass Spectrometry Based Protein Identification by GPU

Massive parallelization of combinatorial statistical genetics analyses porting machine learning methods on general purpose graphics processing units (GPU)

Accelerating the Smith-Waterman Algorithm for Bio-sequence Matching on GPU

High-Throughput parallel blind Virtual Screening using BINDSURF

Hotspot Analysis Based Partial CUDA Acceleration of HMMER 3.0 on GPGPUs

GPU accelerated QTL detection

Recent source codes

Kokkidio: Kokkos+Eigen - write fast, readable multi-platform code

LLaMA-Inference-Bench

MATAR

Over-synchronization in GPU Programs

profile_util: simple C++ library to report memory, timing, thread affinity

MaC: Mamba CPU performance predictor

Mixed-precision finite element kernels

SHMT: The Simultaneous and Heterogenous Multithreading project

Superpipeline: A Universal Approach for Reducing GPU Memory Usage in Large Models

EnergyUCB-Bandit

Most viewed papers (last 30 days)