high performance computing on graphics processing units: hgpu.org

hgpu.org » Bioinformatics

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

View

Download (PDF)

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

View

Download (PDF)

Source codes

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

May 25, 2014 by hgpu

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

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

View

Download (PDF)

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

View

Download (PDF)

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

Entropy-based High Performance Computation of Boolean SNP-SNP Interactions Using GPUs

Carlos Riveros, Manuel Ujaldon, Moscato Pablo

View

Download (PDF)

Tags: Bioinformatics, Biology, CUDA, nVidia, nVidia GeForce GTX 480, Tesla C1060, Tesla C2050

May 12, 2014 by hgpu

Accelerating the scoring module of mass spectrometry-based peptide identification using GPUs

You Li, Hao Chi, Leihao Xia, Xiaowen Chu

View

Download (PDF)

Tags: Bioinformatics, Biology, CUDA, GPU cluster, nVidia, nVidia GeForce GTX 580, Spectrometry

May 12, 2014 by hgpu

GAMUT: GPU accelerated microRNA analysis to uncover target genes through CUDA-miRanda

Shuang Wang, Jihoon Kim, Xiaoqian Jiang, Stefan F Brunner, Lucila Ohno-Machado

View

Download (PDF)

Source codes

Tags: Bioinformatics, Biology, CUDA, nVidia, Package, RNA, Smith-Waterman algorithm, Tesla M2090

May 10, 2014 by hgpu

Exercising high-level parallel programming on streams: a systems biology use case

Marco Aldinucci, Maurizio Drocco, Guilherme Peretti Pezzi, Claudia Misale, Fabio Tordini, Massimo Torquati

View

Download (PDF)

Tags: Bioinformatics, Biology, Cloud, CUDA, Monte Carlo simulation, nVidia, Tesla K40

April 30, 2014 by hgpu

On the Use of Remote GPUs and Low-Power Processors for the Acceleration of Scientific Applications

A. Castello, J. Duato, R. Mayo, A. J. Pena, E. S. Quintana-Orti, V. Roca, F. Silla

View

Download (PDF)

Tags: Bioinformatics, Computer science, CUDA, Energy-efficient computing, Heterogeneous systems, Molecular dynamics, nVidia, nVidia GeForce GTX 480, Virtualization

April 27, 2014 by hgpu

New Efficient Method To Solve Longest Overlap Region Problem For Noncoding DNA Sequence

Yukun Zhong, ZhiWei He, XianHong Wang, Liao Gang

View

Download (PDF)

Tags: Algorithms, Bioinformatics, Biology, CUDA, nVidia, nVidia GeForce GT 610 M

April 16, 2014 by hgpu

A Way For Accelerating The DNA Sequence Reconstruction Problem By CUDA

Yukun Zhong, ZhiWei He, XianHong Wang, XiongBin Cao

View

Download (PDF)

Tags: Algorithms, Bioinformatics, Biology, CUDA, nVidia, nVidia GeForce GT 610 M, Sorting

April 16, 2014 by hgpu

MaxSSmap: A GPU program for short read mapping with the maximum scoring subsequence

Usman Roshan

View

Download (PDF)

Tags: Bioinformatics, Biology, CUDA, nVidia, Short read mapping, Smith-Waterman algorithm, Tesla M2050

March 12, 2014 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

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

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

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

Entropy-based High Performance Computation of Boolean SNP-SNP Interactions Using GPUs

Accelerating the scoring module of mass spectrometry-based peptide identification using GPUs

GAMUT: GPU accelerated microRNA analysis to uncover target genes through CUDA-miRanda

On the Use of Remote GPUs and Low-Power Processors for the Acceleration of Scientific Applications

New Efficient Method To Solve Longest Overlap Region Problem For Noncoding DNA Sequence

A Way For Accelerating The DNA Sequence Reconstruction Problem By CUDA

MaxSSmap: A GPU program for short read mapping with the maximum scoring subsequence

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)