high performance computing on graphics processing units: hgpu.org

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hgpu.org » Applications » Biology

Accelerated cryo-EM structure determination with parallelisation using GPUs in relion-2

Dari Kimanius, Bjorn O Forsberg, Sjors HW Scheres, Erik Lindahl

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Tags: Biology, Cryo-EM, CUDA, Image processing, nVidia, nVidia GeForce GTX 1080, nVidia GeForce GTX 980 Ti

July 5, 2016 by hgpu

PROJECTION Algorithm for Motif Finding on GPUs

Jhoirene B. Clemente, Francis George C. Cabarle, Henry N. Adorna

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Tags: Algorithms, Biology, Computational biology, CUDA, nVidia

May 26, 2016 by hgpu

sPEGG: high throughput eco-evolutionary simulations on commodity graphics processors

Kenichi W. Okamoto, Priyanga Amarasekare

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Tags: Biology, CUDA, Genetics, nVidia, nVidia GeForce GTX 690, Package

April 3, 2016 by hgpu

A Massively Parallel Algorithm for Cell Classification Using CUDA

Samuel Schmidt

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Tags: Bioinformatics, Biology, CUDA, Machine learning, nVidia, nVidia GeForce GTX 770, RNA, Thesis

March 20, 2016 by hgpu

Accelerating Wright-Fisher Forward Simulations on the Graphics Processing Unit

David S. Lawrie

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Tags: Algorithms, Biology, CUDA, Genetics, nVidia, nVidia GeForce GTX 780 M, nVidia GeForce GTX 980

March 10, 2016 by hgpu

GeNN: a code generation framework for accelerated brain simulations

Esin Yavuz, James Turner, Thomas Nowotny

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Tags: Biology, Code generation, CUDA, Neural networks, Neuroscience, Numerical simulation, nVidia, nVidia Quadro K 2000 M, Package, Tesla C2070, Tesla K40

January 29, 2016 by hgpu

Pairwise Sequence Alignment with Gaps with GPU

Thomas C. Carroll, Jude-Thaddeus Ojiaku, Prudence W.H. Wong

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Tags: Algorithms, Bioinformatics, Biology, CUDA, nVidia, nVidia GeForce GTX 650, OpenCL, Sequence alignment

October 27, 2015 by hgpu

Neurokernel: An Open Source Platform for Emulating the Fruit Fly Brain

Lev E. Givon, Aurel A. Lazar

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Tags: Biology, Computer science, CUDA, nVidia, OpenMPI, Tesla K20

October 22, 2015 by hgpu

Accelerating Protein Structure Prediction using Particle Swarm Optimization on GPU

Hamed Khakzad, Yasaman Karami, Seyed Shahriar Arab

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Tags: Algorithms, Bioinformatics, Biology, CUDA, nVidia, Particle swarm optimization, Sequence alignment, Tesla C1060

July 24, 2015 by hgpu

Multiple String Matching on a GPU using CUDAs

Charalampos S. Kouzinopoulos, Panagiotis D. Michailidis, Konstantinos G. Margaritis

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Tags: Algorithms, Biology, Computer science, CUDA, nVidia, nVidia GeForce GTX 280, String matching

July 10, 2015 by hgpu

Modelling the Formation of Ordered Acentrosomal Microtubule Arrays

Alexander Ross Mace

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Tags: Biology, Computer science, Monte Carlo simulation, OpenCL, Probability, Thesis

July 3, 2015 by hgpu

Improving the Mapping of Smith-Waterman Sequence Database Searches onto CUDA-Enabled GPUs

Liang-Tsung Huang, Chao-Chin Wu, Lien-Fu Lai, Yun-Ju Li

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Tags: Bioinformatics, Biology, CUDA, Databases, nVidia, Sequence alignment, Smith-Waterman algorithm, Tesla C1060, Tesla K20

June 30, 2015 by hgpu

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DeepMon: Mobile GPU-based Deep Learning Framework for Continuous Vision Applications

OpenAdSCL

Scalar collapse in AdS with an OpenCL open source code

Rgtsvm: Support Vector Machines on a GPU in R

Kapre: On-GPU Audio Preprocessing Layers for a Quick Implementation of Deep Neural Network Models with Keras

gloo: Collective communications library with various primitives for multi-machine training

Accurate, Large Minibatch SGD: Training ImageNet in 1 Hour

MobiRNN: Efficient Recurrent Neural Network Execution on Mobile GPU

CELES: CUDA-accelerated electromagnetic scattering by large ensembles of spheres

CELES: CUDA-accelerated simulation of electromagnetic scattering by large ensembles of spheres

Boda: A C++ Framework for Efficient Experiments in Computer Vision [WIP]

Implementing Efficient, Portable Computations for Machine Learning

Parallel and in-process compilation of individuals for genetic programming on GPU

ESPRESO: Highly Parallel Solvers for Engineering Applications

Intel Xeon Phi acceleration of Hybrid Total FETI solver

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high performance computing on graphics processing units: hgpu.org

Applications

Accelerated cryo-EM structure determination with parallelisation using GPUs in relion-2

PROJECTION Algorithm for Motif Finding on GPUs

sPEGG: high throughput eco-evolutionary simulations on commodity graphics processors

A Massively Parallel Algorithm for Cell Classification Using CUDA

Accelerating Wright-Fisher Forward Simulations on the Graphics Processing Unit

GeNN: a code generation framework for accelerated brain simulations

Pairwise Sequence Alignment with Gaps with GPU

Neurokernel: An Open Source Platform for Emulating the Fruit Fly Brain

Accelerating Protein Structure Prediction using Particle Swarm Optimization on GPU

Multiple String Matching on a GPU using CUDAs

Modelling the Formation of Ordered Acentrosomal Microtubule Arrays

Improving the Mapping of Smith-Waterman Sequence Database Searches onto CUDA-Enabled GPUs

Recent source codes

DeepMon: Mobile GPU-based Deep Learning Framework for Continuous Vision Applications

OpenAdSCL

Rgtsvm: Support Vector Machines on a GPU in R

Kapre: On-GPU Audio Preprocessing Layers for a Quick Implementation of Deep Neural Network Models with Keras

gloo: Collective communications library with various primitives for multi-machine training

MobiRNN: Efficient Recurrent Neural Network Execution on Mobile GPU

CELES: CUDA-accelerated electromagnetic scattering by large ensembles of spheres

Boda: A C++ Framework for Efficient Experiments in Computer Vision [WIP]

Parallel and in-process compilation of individuals for genetic programming on GPU

ESPRESO: Highly Parallel Solvers for Engineering Applications

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Featured events

4th International Conference on Biomedical and Bioinformatics Engineering (ICBBE), 2017

9th International Conference on Signal Processing Systems (ICSPS), 2017

The 5th International conference on Control, Mechatronics and Automation (ICCMA), 2017

8th International Conference on Biology, Environment and Chemistry (ICBEC), 2017

2nd International Conference on Communication and Information Systems (ICCIS), 2017