high performance computing on graphics processing units: hgpu.org

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hgpu.org » Applications » Biology

Accelerating calculations of RNA secondary structure partition functions using GPUs

Harry A Stern, David H Mathews

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Tags: Bioinformatics, Biology, CUDA, nVidia, Package, RNA, Tesla M2050

November 11, 2013 by hgpu

Computational kinetics of a large scale biological process on GPU workstations: DNA bending

Arnold Peter Ruymgaart

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Tags: Biology, CUDA, Molecular dynamics, nVidia, nVidia GeForce GTX 480, Thesis

November 8, 2013 by hgpu

Communication Optimization for Multi GPU Implementation of Smith-Waterman Algorithm

Sampath Kumar, P. K. Baruah

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Tags: Algorithms, Biology, Computational biology, CUDA, Databases, nVidia, Sequence matching, Smith-Waterman algorithm, Tesla M2050

November 2, 2013 by hgpu

gEMpicker: A Highly Parallel GPU-Accelerated Particle Picking Tool for Cryo-Electron Microscopy

Thai V. Hoang, Xavier Cavin, Patrick Schultz, David W. Ritchie

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Tags: Algorithms, Biology, Cryo-EM, CUDA, Electron microscopy, FFT, Macromolecule, Microscopy, nVidia, Tesla C1060, Tesla C2075

October 24, 2013 by hgpu

cudaMap: a GPU accelerated program for gene expression connectivity mapping

Darragh G McArt, Peter Bankhead, Philip D Dunne, Manuel Salto-Tellez, Peter Hamilton, Shu-Dong Zhang

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

October 17, 2013 by hgpu

High performance sequence mining using pairwise statistical significance

Yuhong Zhang, Feng Chen

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

October 12, 2013 by hgpu

Regional Heritability Advanced Complex Trait Analysis for GPU and Traditional Parallel Architectures

L. Cebamanos, A. Gray, I. Stewart, A. Tenesa

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Tags: Algorithms, Bioinformatics, Biology, CUDA, nVidia, Tesla K20

October 12, 2013 by hgpu

Enabling the use of Heterogeneous Computing for Bioinformatics

Ramakrishna Bijanapalli Chakri

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Tags: Bioinformatics, Biology, CUDA, FPGA, Heterogeneous systems, nVidia, nVidia GeForce GTX 580, Smith-Waterman algorithm, Thesis

October 8, 2013 by hgpu

GPU-powered Simulation Methodologies for Biological Systems

Daniela Besozzi, Giulio Caravagna, Paolo Cazzaniga, Marco Nobile, Dario Pescini, Alessandro Re

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Tags: Biology, Computer science, CUDA, nVidia

October 2, 2013 by hgpu

gEMfitter: A Highly Parallel FFT-Based 3D Density Fitting Tool With GPU Texture Memory Acceleration

Thai V. Hoang, Xavier Cavin, David W. Ritchie

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Tags: Biology, Cryo-EM, CUDA, Electron microscopy, FFT, Macromolecule, Microscopy, nVidia, Tesla C2075

September 28, 2013 by hgpu

Improving Resource Utilization in Heterogeneous CPU-GPU Systems

Michael Boyer

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Tags: Algorithms, ATI, ATI Radeon HD 5870, ATI Radeon HD 7970, Biology, Computer science, CUDA, Heterogeneous systems, nVidia, nVidia GeForce GTX 280, OpenCL, Package, Software Engineering, Thesis

September 23, 2013 by hgpu

A Novel CPU/GPU Simulation Environment for Large-Scale Biologically-Realistic Neural Modeling

Roger V. Hoang, Devyani Tanna, Laurence C. Jayet Bray, Sergiu M. Dascalu, Frederick C. Harris Jr.

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Tags: Biology, CUDA, Neural networks, Neuroscience, nVidia, nVidia GeForce GTX 460, nVidia GeForce GTX 480, nVidia GeForce GTX 680, Package, Tesla C2050

September 14, 2013 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

Accelerating calculations of RNA secondary structure partition functions using GPUs

Computational kinetics of a large scale biological process on GPU workstations: DNA bending

Communication Optimization for Multi GPU Implementation of Smith-Waterman Algorithm

gEMpicker: A Highly Parallel GPU-Accelerated Particle Picking Tool for Cryo-Electron Microscopy

cudaMap: a GPU accelerated program for gene expression connectivity mapping

High performance sequence mining using pairwise statistical significance

Regional Heritability Advanced Complex Trait Analysis for GPU and Traditional Parallel Architectures

Enabling the use of Heterogeneous Computing for Bioinformatics

GPU-powered Simulation Methodologies for Biological Systems

gEMfitter: A Highly Parallel FFT-Based 3D Density Fitting Tool With GPU Texture Memory Acceleration

Improving Resource Utilization in Heterogeneous CPU-GPU Systems

A Novel CPU/GPU Simulation Environment for Large-Scale Biologically-Realistic Neural Modeling

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