high performance computing on graphics processing units: hgpu.org

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hgpu.org » Applications » Biology

Interactive GPU active contours for segmenting inhomogeneous objects

Chris G. Willcocks, Philip T. G. Jackson, Carl J. Nelson, Amar V. Nasrulloh, Boguslaw Obara

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Tags: Biology, Image processing, Medicine, nVidia, nVidia GeForce GTX Titan X, OpenCL, Package

February 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

Accelerating Genomics Research with OpenCL and FPGAs

Chris Rauer, George S. Powley, Mir Ahsan, Nicholas Finamore

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Tags: Algorithms, Biology, Computer science, FPGA, Genomics, OpenCL

October 15, 2017 by hgpu

Dynamic Parallelism in GPU Optimized Barnes Hut Trees for Molecular Dynamics Simulations

Melisa Carranza Zuniga

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Tags: Algorithms, Biology, Biomolecules, Biophysics, Chemistry, CUDA, Molecular dynamics, nVidia, nVidia GeForce GTX 480, Physics, Thesis

August 26, 2017 by hgpu

eccCL: parallelized GPU implementation of Ensemble Classifier Chains

Mona Riemenschneider, Alexander Herbst, Ari Rasch, Sergei Gorlatch, Dominik Heider

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Tags: Biology, Computer science, Java, Next-Generation sequencing, nVidia, OpenCL, Package, R, Tesla K20

August 26, 2017 by hgpu

Simulating the Cardinal Movements of Childbirth Using Finite Element Analysis on the Graphics Processing Unit

Zelimkhan Gerikhanov

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Tags: AMD Radeon HD 8970 M, ATI, Biology, Biomechanics, FEM, Finite element method, Medicine, MRI, OpenCL, Thesis

August 17, 2017 by hgpu

Gpufit: An open-source toolkit for GPU-accelerated curve fitting

Adrian Przybylski, Bjorn Thiel, Jan Keller-Findeisen, Bernd Stock, Mark Bates

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Tags: Biology, Computer science, CUDA, Microscopy, nVidia, nVidia GeForce GTX 1080, Package, Python

August 17, 2017 by hgpu

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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

Equalizer 2.0: Convergence of a Parallel Rendering Framework

Equalizer 2.0 – Convergence of a Parallel Rendering Framework

QMCPACK: An open source ab initio Quantum Monte Carlo package for the electronic structure of atoms, molecules, and solids

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high performance computing on graphics processing units: hgpu.org

Applications

Interactive GPU active contours for segmenting inhomogeneous objects

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

Accelerating Genomics Research with OpenCL and FPGAs

Dynamic Parallelism in GPU Optimized Barnes Hut Trees for Molecular Dynamics Simulations

eccCL: parallelized GPU implementation of Ensemble Classifier Chains

Simulating the Cardinal Movements of Childbirth Using Finite Element Analysis on the Graphics Processing Unit

Gpufit: An open-source toolkit for GPU-accelerated curve fitting

Recent source codes

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

Equalizer 2.0: Convergence of a Parallel Rendering Framework

QMCPACK: An open source ab initio Quantum Monte Carlo package for the electronic structure of atoms, molecules, and solids

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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