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ASW: Accelerating Smith-Waterman Algorithm on Coupled CPU-GPU Architecture

Huihui Zou, Shanjiang Tang, Ce Yu, Hao Fu, Yusen Li, Wenjie Tang

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Tags: Algorithms, APU, Bioinformatics, Biology, CUDA, Heterogeneous systems, nVidia, nVidia GeForce GTX 750, OpenCL, Sequence alignment, Smith-Waterman algorithm

December 9, 2018 by hgpu

Fast and Flexible GPU Accelerated Binding Free Energy Calculations within the AMBER Molecular Dynamics Package

Daniel J. Mermelstein, Charles Lin, Gard Nelson, Rachael Kretsch, J. Andrew McCammon, Ross C. Walker

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Tags: Algorithms, Bioinformatics, Biology, CUDA, Molecular dynamics, nVidia, nVidia GeForce GTX 1080 Ti, nVidia GeForce GTX Titan X

January 20, 2018 by hgpu

pyPaSWAS: Python-based multi-core CPU and GPU sequence alignment

Sven Warris, N. Roshan N. Timal, Marcel Kempenaar, Arne M. Poortinga, Henri van de Geest, Ana L. Varbanescu, Jan-Peter Nap

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Tags: Bioinformatics, Biology, CUDA, nVidia, nVidia GeForce GTX 1070, OpenCL, Package, Python, Sequence alignment, Smith-Waterman algorithm

January 13, 2018 by hgpu

Molecular dynamics recipes for genome research

Tommaso Biagini, Giovanni Chillemi, Gianluigi Mazzoccoli, Alessandro Grottesi, Caterina Fusilli, Daniele Capocefalo, Stefano Castellana, Angelo Luigi Vescovi, Tommaso Mazza

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Tags: Benchmarking, Bioinformatics, Biology, Chemistry, CUDA, Genomics, Molecular dynamics, nVidia, OpenCL, Physics, Tesla C2070

December 19, 2017 by hgpu

HCudaBLAST: an implementation of BLAST on Hadoop and Cuda

Nilay Khare, Alind Khare and Farhan Khan

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Tags: Algorithms, Bioinformatics, Biology, BLAST, CUDA, Hadoop, nVidia, nVidia Quadro 2000, nVidia Quadro 600, Tesla C2075

December 3, 2017 by hgpu

A Hybrid-parallel Architecture for Applications in Bioinformatics

Jan Christian Kassens

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Tags: Algorithms, Bioinformatics, Biology, Computer science, CUDA, FPGA, nVidia, nVidia GeForce GTX 780 Ti, Thesis

December 3, 2017 by hgpu

High Performance Streaming Smith-Waterman Implementation with Implicit Synchronization on Intel FPGA using OpenCL

Ernst Joachim Houtgast, Vlad-Mihai Sima, Zaid Al-Ars

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Tags: Algorithms, Bioinformatics, Biology, FPGA, OpenCL, Smith-Waterman algorithm

November 26, 2017 by hgpu

A Study of Time and Energy Efficient Algorithms for Parallel and Heterogeneous Computing

Jude-Thaddeus Ojiaku

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Tags: ATI, ATI Radeon HD 7750, ATI Radeon HD 7970, Bioinformatics, Computer science, Graph layout, Heterogeneous systems, nVidia, nVidia GefForce GTX 650, nVidia GefForce GTX 680, OpenCL, Thesis

October 29, 2017 by hgpu

Smith-Waterman Acceleration in Multi-GPUs: A Performance per Watt Analysis

Jesus Perez Serrano, Edans Flavius De Oliveira Sandes, Alba Cristina Magalhaes Alves de Melo, Manuel Ujaldon

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Tags: Bioinformatics, Biology, CUDA, Energy-efficient computing, nVidia, nVidia GeForce GTX 980, Performance, Smith-Waterman algorithm

June 10, 2017 by hgpu

Exploiting Multi-level Parallelism on a Many-core System for the Application of Hyperheuristics to a Molecular Docking Problem

Jose M. Cecilia, Jose-Matias, Cutillas-Lozano, Domingo Gimenez, Baldomero Imbernon

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Tags: Bioinformatics, Biology, Chemistry, Intel Xeon Phi, Metaheuristics, molecular docking

March 20, 2017 by hgpu

First Experiences Optimizing Smith-Waterman on Intel’s Knights Landing Processor

Enzo Rucci, Carlos Garcia, Guillermo Botella, Armando De Giusti, Marcelo Naiouf, Manuel Prieto-Matias

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Tags: Bioinformatics, Biology, Computer science, Intel Xeon Phi, Sequence alignment, Smith-Waterman algorithm

February 26, 2017 by hgpu

Analysis and implementation of a BLAST-Like algorithm for MIC architectures

Felipe Sulser Larraz

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Tags: Benchmarking, Bioinformatics, Biology, Computer science, Databases, Filtering, Intel Xeon Phi, Sequence alignment, Smith-Waterman algorithm, Thesis

February 2, 2017 by hgpu

libhclooc: Software Library Facilitating Out-of-core Implementations of Accelerator Kernels on Hybrid Computing Platforms

Novel Data-Partitioning Algorithms for Performance and Energy Optimization of Data-Parallel Applications on Modern Heterogeneous HPC Platforms

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high performance computing on graphics processing units: hgpu.org

ASW: Accelerating Smith-Waterman Algorithm on Coupled CPU-GPU Architecture

Fast and Flexible GPU Accelerated Binding Free Energy Calculations within the AMBER Molecular Dynamics Package

pyPaSWAS: Python-based multi-core CPU and GPU sequence alignment

Molecular dynamics recipes for genome research

HCudaBLAST: an implementation of BLAST on Hadoop and Cuda

A Hybrid-parallel Architecture for Applications in Bioinformatics

High Performance Streaming Smith-Waterman Implementation with Implicit Synchronization on Intel FPGA using OpenCL

A Study of Time and Energy Efficient Algorithms for Parallel and Heterogeneous Computing

Smith-Waterman Acceleration in Multi-GPUs: A Performance per Watt Analysis

Exploiting Multi-level Parallelism on a Many-core System for the Application of Hyperheuristics to a Molecular Docking Problem

First Experiences Optimizing Smith-Waterman on Intel’s Knights Landing Processor

Analysis and implementation of a BLAST-Like algorithm for MIC architectures

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7th International Workshop on OpenCL, 2019

Distributed Heterogeneous Programming in C/C++ (DHPCC++), 2019

3rd International Workshop on Theoretical Approaches to Performance Evaluation, Modeling and Simulation (TAPEMS), 2019

International Conference on Frontiers of Neural Networks (ICFNN), 2019

International Conference on Frontiers of Artificial Intelligence and Machine Learning (FAIML), 2019