high performance computing on graphics processing units: hgpu.org

hgpu.org » Bioinformatics

Flexible, Fast and Accurate Sequence Alignment Profiling on GPGPU with PaSWAS

Sven Warris, Feyruz Yalcin, Katherine J. L. Jackson, Jan Peter Nap

View

Download (PDF)

Source codes

Tags: Bioinformatics, Biology, CUDA, nVidia, nVidia GeForce GTX 285, nVidia GeForce GTX 295, Package, Sequence alignment, Smith-Waterman algorithm, Tesla C1060

April 7, 2015 by hgpu

Arioc: high-throughput read alignment with GPU-accelerated exploration of the seed-and-extend search space

Richard Wilton, Tamas Budavari, Ben Langmead, Sarah J. Wheelan, Steven L. Salzberg, Alexander S. Szalay

View

Download (PDF)

Source codes

Tags: Bioinformatics, Biology, CUDA, nVidia, Package, Sequence alignment, Tesla K20

March 28, 2015 by hgpu

Parallelization, Scalability, and Reproducibility in Next-Generation Sequencing Analysis

Johannes Koster

View

Download (PDF)

Source codes

Tags: Algorithms, Bayesian, Bioinformatics, Biology, Filtering, Next-Generation sequencing, nVidia, nVidia GeForce GTX 580, nVidia GeForce GTX 780, OpenCL, Package, Thesis

March 23, 2015 by hgpu

Implementation of Smith-Waterman algorithm in OpenCL for GPUs

Dzmitry Razmyslovich, Guillermo Marcus, Markus Gipp, Marc Zapatka, Andreas Szillus

View

Download (PDF)

Source codes

Tags: Bioinformatics, Biology, nVidia, nVidia GeForce GTX 480, OpenCL, Package, Sequence alignment, Smith-Waterman algorithm

February 27, 2015 by azhar ali

NMF-mGPU: non-negative matrix factorization on multi-GPU systems

Edgardo Mejia-Roa, Daniel Tabas-Madrid, Javier Setoain, Carlos Garcia, Francisco Tirado, Alberto Pascual-Montano

View

Download (PDF)

Source codes

Tags: Algorithms, Bioinformatics, Biology, CUDA, Factorization, GPU cluster, MPI, Nonnegative matrix factorization, nVidia, Package, Tesla C1060

February 19, 2015 by hgpu

Massively parallel read mapping on GPUs with the q-group index and PEANUT

Johannes Koster, Sven Rahmann

View

Download (PDF)

Tags: Algorithms, Bioinformatics, Biology, nVidia, nVidia GeForce GTX 780, OpenCL

October 20, 2014 by hgpu

Mapping dynamic programming algorithms on graphics processing units

Muhammad Kashif Hanif

View

Download (PDF)

Tags: Algorithms, Bioinformatics, Computer science, CUDA, nVidia, nVidia GeForce GTX 560 Ti, Thesis

October 11, 2014 by hgpu

Accelerating Protein Coordinate Conversion using GPUs

Mahsa Bayati, Jaydeep P. Bardhan, David M. King, Miriam Leeser

View

Download (PDF)

Tags: Algorithms, Bioinformatics, Biology, CUDA, nVidia, Tesla C2075

October 10, 2014 by hgpu

A massively parallel algorithm for constructing the BWT of large string sets

Jacopo Pantaleoni

View

Download (PDF)

Tags: Algorithms, Bioinformatics, Computer science, CUDA, nVidia, Tesla K40

October 4, 2014 by hgpu

Calculation of Force Field Grids for Molecular Docking Using Graphics Processing Unit

Mikhail A. Farkov

View

Download (PDF)

Tags: Algorithms, Bioinformatics, Biology, CUDA, molecular docking, nVidia, nVidia GeForce GT 440, Tesla K20, Tesla M2090

September 24, 2014 by hgpu

Parallel Computation of Non-Bonded Interactions in Drug Discovery: Nvidia GPUs vs. Intel Xeon Phi

Jianbin Fang, Ana Lucia Varbanescu, Baldomero Imbernon, Jose M. Cecilia, Horacio Perez-Sanchez

View

Download (PDF)

Tags: Bioinformatics, Biology, CUDA, Electrostatics, Intel Xeon Phi, nVidia, Performance, Pharmaceuticals, Tesla K20

September 13, 2014 by hgpu

Convex Clustering: An Attractive Alternative to Hierarchical Clustering

Gary K. Chen, Eric Chi, John Ranola, Kenneth Lange

View

Download (PDF)

Source codes

Tags: Algorithms, Bioinformatics, Biology, Cluster analysis, Clustering, Genomics, Hierarchical clustering, nVidia, OpenCL, Package, Tesla C2050

September 9, 2014 by hgpu

Coccinelle: a C code transformation engine using SmPL for matches, refactorings, and bug fixing

Advances in Semantic Patching for HPC-oriented Refactorings with Coccinelle

DuoReduce: MLIR's benchmark

Hardware-Assisted Software Testing and Debugging for Heterogeneous Computing

Shamrock: Multi-GPU hydrodynamics for astrophysics

The Shamrock code: I- Smoothed Particle Hydrodynamics on GPUs

LLMPerf: GPU Performance Modeling meets Large Language Models

Hercules: A Compiler for Productive Programming of Heterogeneous Systems

* * *

high performance computing on graphics processing units: hgpu.org

Flexible, Fast and Accurate Sequence Alignment Profiling on GPGPU with PaSWAS

Arioc: high-throughput read alignment with GPU-accelerated exploration of the seed-and-extend search space

Parallelization, Scalability, and Reproducibility in Next-Generation Sequencing Analysis

Implementation of Smith-Waterman algorithm in OpenCL for GPUs

NMF-mGPU: non-negative matrix factorization on multi-GPU systems

Massively parallel read mapping on GPUs with the q-group index and PEANUT

Mapping dynamic programming algorithms on graphics processing units

Accelerating Protein Coordinate Conversion using GPUs

A massively parallel algorithm for constructing the BWT of large string sets

Calculation of Force Field Grids for Molecular Docking Using Graphics Processing Unit

Parallel Computation of Non-Bonded Interactions in Drug Discovery: Nvidia GPUs vs. Intel Xeon Phi

Convex Clustering: An Attractive Alternative to Hierarchical Clustering

Recent source codes

Coccinelle: a C code transformation engine using SmPL for matches, refactorings, and bug fixing

DuoReduce: MLIR's benchmark

Shamrock: Multi-GPU hydrodynamics for astrophysics

LLMPerf: GPU Performance Modeling meets Large Language Models

Hercules: A Compiler for Productive Programming of Heterogeneous Systems

Celerity Runtime: High-level C++ for Accelerator Clusters

wgpy: WebGL accelerated numpy-compatible array library for web browser

Microbenchmarking OpenMP target offload with Catch2

SUperman: Highly Efficient Permanent Computation Library

TransCL: An Automatic CUDA-to-OpenCL Programs Transformation Framework

Most viewed papers (last 30 days)