high performance computing on graphics processing units: hgpu.org

hgpu.org » Biology

Accelerating Protein Sequence Search in a Heterogeneous Computing System

Shucai Xiao, Heshan Lin, Wu-chun Feng

View

Tags: Algorithms, Bioinformatics, Biology, BLAST, Databases, Heterogeneous systems, nVidia, Optimization, Tesla C1060, Tesla C2050

November 23, 2011 by hgpu

Application of GPGPU for Acceleration of Short DNA Sequence Alignment in Unipro UGENE Project

Konstantin Okonechinkov, German Grekhov, Konstantin Stepanyuk, Mikhail Fursov

View

Download (PDF)

Source codes

Tags: Algorithms, Bioinformatics, Biology, nVidia, OpenCL, Package, Sequence alignment, Tesla C1060, Tesla C2070

November 22, 2011 by hgpu

Using Graphics Processors for a High Performance Normalization of Gene Expressions

Andres Rodriguez, Oswaldo Trelles, Manuel Ujaldon

View

Download (PDF)

Tags: Bioinformatics, Biology, CUDA, nVidia, nVidia GeForce 9800 GX2

November 22, 2011 by hgpu

Parallel Approach for Longest Common Subsequence problem on GPU

Raik Issaoui, Amine Draief, Abdelfettah Belghith

View

Download (PDF)

Tags: Algorithms, Bioinformatics, Biology, CUDA, nVidia, nVidia GeForce GT 430, OpenCL, Sequence matching

November 16, 2011 by hgpu

High-performance Blob-based iterative reconstruction of electron tomography on multi-GPUs

Xiaohua Wan, Fa Zhang, Qi Chu, Zhiyong Liu

View

Download (PDF)

Tags: Biology, CUDA, Image reconstruction, nVidia, nVidia GeForce GTX 295, OpenMP, Tomography

November 15, 2011 by hgpu

An Ultrafast Scalable Many-core Motif Discovery Algorithm for Multiple GPUs

Yongchao Liu, Bertil Schmidt, Douglas L. Maskell

View

Download (PDF)

Source codes

Tags: Algorithms, Benchmarking, Biology, CUDA, GPU cluster, MPI, nVidia, OpenMP, Package, Tesla S2050

November 15, 2011 by hgpu

Advantages and GPU implementation of high-performance indexed DNA search based on suffix arrays

Gustavo Encarnacao, Nuno Sebastiao, Nuno Roma

View

Download (PDF)

Tags: Bioinformatics, Biology, CUDA, nVidia, nVidia GeForce GTX 580, Suffix trees

November 13, 2011 by hgpu

Molecular Docking on FPGA and GPU Platforms

I. Pechan, B. Feher

View

Download (PDF)

Tags: Algorithms, Bioinformatics, Biology, CUDA, FPGA, nVidia, nVidia GeForce GT 220, nVidia GeForce GTX 260

November 13, 2011 by hgpu

GSNP: A DNA Single-Nucleotide Polymorphism Detection System with GPU Acceleration

Mian Lu, Jiuxin Zhao, Qiong Luo, Bingqiang Wang, Shaohua Fu, Zhe Lin

View

Download (PDF)

Source codes

Tags: Bioinformatics, Biology, Compression, nVidia, Package, Sorting, Tesla M2050

November 12, 2011 by hgpu

Bit-Parallel Multiple Pattern Matching

Tuan Tu Tran, Mathieu Giraud, Jean-Stephane Varre

View

Download (PDF)

Tags: Algorithms, ATI, ATI Radeon HD 5870, Biology, Computational biology, nVidia, nVidia GeForce GTX 480, OpenCL

November 10, 2011 by hgpu

Improving CUDASW++, a Parallelization of Smith-Waterman for CUDA Enabled Devices

Doug Hains, Zach Cashero, Mark Ottenberg, Wim Bohm, Sanjay Rajopadhye

View

Download (PDF)

Tags: Algorithms, Bioinformatics, Biology, CUDA, nVidia, Sequence alignment, Smith-Waterman algorithm, Tesla C1060, Tesla C2050

November 5, 2011 by hgpu

Effective Parallelization of Non-bonded Interactions Kernel for Virtual Screening on GPUs

Gines D. Guerrero, Horacio Perez-Sanchez, Wolfgang Wenzel, Jose M. Cecilia, Jose M. Garcia

View

Download (PDF)

Tags: Bioinformatics, Biology, CUDA, nVidia, Optimization, Pharmaceuticals, Tesla C1060

October 30, 2011 by hgpu

WiLLM: An Open Wireless LLM Communication System

Vcc: the Vulkan Clang Compiler

No More Shading Languages: Compiling C++ to Vulkan Shaders

hpcbench: A set of benchmarking utilities for biomolecular simulation tools

Engineering Supercomputing Platforms for Biomolecular Applications

HPCTransCompile: An AI Compiler Generated Dataset for High-Performance CUDA Transpilation and LLM Preliminary Exploration

* * *

high performance computing on graphics processing units: hgpu.org

Accelerating Protein Sequence Search in a Heterogeneous Computing System

Application of GPGPU for Acceleration of Short DNA Sequence Alignment in Unipro UGENE Project

Using Graphics Processors for a High Performance Normalization of Gene Expressions

Parallel Approach for Longest Common Subsequence problem on GPU

High-performance Blob-based iterative reconstruction of electron tomography on multi-GPUs

An Ultrafast Scalable Many-core Motif Discovery Algorithm for Multiple GPUs

Advantages and GPU implementation of high-performance indexed DNA search based on suffix arrays

Molecular Docking on FPGA and GPU Platforms

GSNP: A DNA Single-Nucleotide Polymorphism Detection System with GPU Acceleration

Bit-Parallel Multiple Pattern Matching

Improving CUDASW++, a Parallelization of Smith-Waterman for CUDA Enabled Devices

Effective Parallelization of Non-bonded Interactions Kernel for Virtual Screening on GPUs

Recent source codes

WiLLM: An Open Wireless LLM Communication System

Vcc: the Vulkan Clang Compiler

hpcbench: A set of benchmarking utilities for biomolecular simulation tools

HPCTransCompile: An AI Compiler Generated Dataset for High-Performance CUDA Transpilation and LLM Preliminary Exploration

chemtrain: Training Molecular Dynamics Potentials in JAX

microSYCL: SYCL micro-benchmarks repository

XaaS containers

CASS: Cuda-Amd aSSembly

Cluser of smartphones for edge computing application using TensorFlow

SYCL Container

Most viewed papers (last 30 days)