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

Usman Roshan

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

March 12, 2014 by hgpu

Parallelization of DNA alignment algorithms using GPUs

Gustavo Encarnacao

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

March 7, 2014 by hgpu

Hybrid Framework for pairwise DNA Sequence Alignment Using the CUDA compatible GPU

H. Khaled, R. El Gohary, N.L. Badr, H. M. Faheem

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Tags: Bioinformatics, Biology, CUDA, nVidia, nVidia GeForce GT 540 M, Sequence alignment, Smith-Waterman algorithm

March 6, 2014 by hgpu

QuickProbs – A Fast Multiple Sequence Alignment Algorithm Designed for Graphics Processors

Adam Gudys, Sebastian Deorowicz

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Tags: ATI, ATI Radeon HD 7970, Bioinformatics, Biology, nVidia, nVidia GeForce GTX 480, nVidia GeForce GTX 580, nVidia GeForce GTX 680, OpenCL, Package, Sequence alignment

March 4, 2014 by hgpu

A Multi GPU Read Alignment Algorithm with Model-based Performance Optimization

Aleksandr Drozd, Naoya Maruyama, Satoshi Matsuoka

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

March 1, 2014 by hgpu

MICA: A fast short-read aligner that takes full advantage of Intel Many Integrated Core Architecture (MIC)

Sze-Hang Chan, Jeanno Cheung, Edward Wu, Heng Wang, Chi-Man Liu, Xiaoqian Zhu, Shaoliang Peng, Ruibang Luo, Tak-Wah Lam

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Tags: Bioinformatics, Biology, Intel Xeon Phi, Package

February 21, 2014 by hgpu

Parallel implementation of 3D protein structure similarity searches using a GPU and the CUDA

Dariusz Mrozek, Milosz Brozek, Bozena Malysiak-Mrozek

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Tags: Algorithms, Bioinformatics, Biology, CUDA, nVidia, nVidia GeForce GTX 285, nVidia GeForce GTX 560 Ti, Package, Tesla C1060

February 4, 2014 by hgpu

GPU-Accelerated BWT Construction for Large Collection of Short Reads

Chi-Man Liu, Ruibang Luo, Tak-Wah Lam

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Tags: Algorithms, Biology, CUDA, nVidia, nVidia GeForce GTX 680

January 30, 2014 by hgpu

Accelerating a Bayesian Phylogenetic Inference Application with OpenACC

Joao Pedro de Matos Neves

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Tags: Bayesian, Bioinformatics, Biology, CUDA, nVidia, nVidia GeForce GTX 580, OpenACC

January 25, 2014 by hgpu

Optimal Alignment of Three Sequences On A GPU

Junjie Li, Sanjay Ranka, Sartaj Sahni

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

January 14, 2014 by hgpu

A tool for mapping Single Nucleotide Polymorphisms using Graphics Processing Units

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

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Tags: Algorithms, Bioinformatics, Biology, CUDA, nVidia, nVidia GeForce GTX 480, Package, Smith-Waterman algorithm, Tesla K20

January 12, 2014 by hgpu

Nengo: a Python tool for building large-scale functional brain models

Trevor Bekolay, James Bergstra, Eric Hunsberger, Travis DeWolf, Terrence C. Stewart, Daniel Rasmussen, Xuan Choo, Aaron Russell Voelker, Chris Eliasmith

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Tags: ATI, ATI Radeon HD 7970, Biology, Neuroscience, nVidia, nVidia GeForce GTX 280, OpenCL, Package, PyOpenCL, Python

January 9, 2014 by hgpu

Fancier High-Performance API

Fancier: A Unified Framework for Java, C, and OpenCL Integration

A Compiler Framework for Optimizing Dynamic Parallelism on GPUs

A Compiler Framework for Optimizing Dynamic Parallelism on GPUs

GPOEO: a micro-intrusive GPU online energy optimization framework for iterative applications

Dynamic GPU Energy Optimization for Machine Learning Training Workloads

CFU Playground: Full-Stack Open-Source Framework for Tiny Machine Learning (tinyML) Acceleration on FPGAs

From Loop Fusion to Kernel Fusion: A Domain-specific Approach to Locality Optimization

System-Level Optimization and Code Generation for Graphics Processors using a Domain-Specific Language

Faster-Mean-Shift-Euc

GPU-accelerated Faster Mean Shift with euclidean distance metrics

Turbo: A constraint solver purely on GPUs (CUDA)

A Variant of Concurrent Constraint Programming on GPU

ProGraML: Program Graphs for Machine Learning

PROGRAML: A Graph-based Program Representation for Data Flow Analysis and Compiler Optimizations

Datoviz: GPU interactive scientific data visualization with Vulkan

High-Performance Interactive Scientific Visualization With Datoviz via the Vulkan Low-Level GPU API

NetKet 3: Machine Learning Toolbox for Many-Body Quantum Systems

NetKet 3: Machine Learning Toolbox for Many-Body Quantum Systems

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