high performance computing on graphics processing units: hgpu.org

Applications

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

View

Download (PDF)

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

View

Download (PDF)

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

View

Download (PDF)

Source codes

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

View

Download (PDF)

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

View

Download (PDF)

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

View

Download (PDF)

Source codes

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

View

Download (PDF)

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

View

Download (PDF)

Source codes

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

View

Download (PDF)

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

View

Download (PDF)

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

View

Download (PDF)

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

View

Download (PDF)

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

June 30, 2015 by hgpu

Page 3 of 39«1 234 5...10 20 30...»Last »

HLS4ML

Fast inference of deep neural networks in FPGAs for particle physics

cytonRL: reinforcement learning, deep Q-network, double DQN, dueling DQN, prioritized experience replay

CytonRL: an Efficient Reinforcement Learning Open-source Toolkit Implemented in C++

DLL: Deep Learning Library (DLL) for C++ (ANNs, CNNs, RBMs, DBNs...)

DLL: A Blazing Fast Deep Neural Network Library

HCC: Open Source, Optimizing C++ Compiler for Heterogeneous Compute for the ROCm GPU Computing Platform

Evaluating Performance Tradeoffs on the Radeon Open Compute Platform

pynufft: Python non-uniform fast Fourier transform (NUFFT)

Python Non-Uniform Fast Fourier Transform (PyNUFFT): An Accelerated Non-Cartesian MRI Package on a Heterogeneous Platform (CPU/GPU)

MALBEC: a new CUDA-C ray-tracer in General Relativity

Volna-OP2: OP2 port of the original Volna code

The VOLNA-OP2 Tsunami Code (Version 1.0)

CuLDA_CGS: Solving Large-scale LDA Problems on GPUs

MeterPU: Generic Portable Measurement Framework for Multicore CPU and Multi-GPU Systems

Programming Abstractions and Optimization Techniques for GPU-based Heterogeneous Systems

GHOST: General, Hybrid and Optimized Sparse Toolkit

Chebyshev Filter Diagonalization on Modern Manycore Processors and GPGPUs

See all packages

* * *

2018

August

06-07

Osaka, Japan

International Conference on Biomedicine & Pharmacotherapy, 2018

2018

June

28-30

Bangkok

8th International Workshop on Computer Science and Engineering (WCSE’18), 2018

2018

October

15-16

Helsinki, Finland

International Conference on Robotics, Artificial Intelligence, Automation and Mechatronics, 2018

2018

June

27-29

No.2 Chong Wen Road, Nan An District, Chongqing 400065, P. R. China

The 3rd IEEE International Conference on Image, Vision and Computing (ICIVC), 2018

2018

June

23-25

Room 301, 2nd Floor, No.2 Teaching Building, West Area of the campus, No. 388 Lumo Road,Wuhan, P.R. China

The 2th International Conference on Robotics and Automation Sciences (ICRAS), 2018

Add event

See all events

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

HLS4ML

cytonRL: reinforcement learning, deep Q-network, double DQN, dueling DQN, prioritized experience replay

DLL: Deep Learning Library (DLL) for C++ (ANNs, CNNs, RBMs, DBNs...)

HCC: Open Source, Optimizing C++ Compiler for Heterogeneous Compute for the ROCm GPU Computing Platform

pynufft: Python non-uniform fast Fourier transform (NUFFT)

MALBEC: a new CUDA-C ray-tracer in General Relativity

Volna-OP2: OP2 port of the original Volna code

CuLDA_CGS: Solving Large-scale LDA Problems on GPUs

MeterPU: Generic Portable Measurement Framework for Multicore CPU and Multi-GPU Systems

GHOST: General, Hybrid and Optimized Sparse Toolkit

Most viewed papers (last 30 days)

Featured events

International Conference on Biomedicine & Pharmacotherapy, 2018

8th International Workshop on Computer Science and Engineering (WCSE’18), 2018

International Conference on Robotics, Artificial Intelligence, Automation and Mechatronics, 2018

The 3rd IEEE International Conference on Image, Vision and Computing (ICIVC), 2018

The 2th International Conference on Robotics and Automation Sciences (ICRAS), 2018