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Faster Algorithms for RNA-folding using the Four-Russians method

Balaji Venkatachalam, Yelena Frid, Dan Gusfield

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Tags: Algorithms, Bioinformatics, Biology, CUDA, nVidia, nVidia GeForce GTX 550 Ti, RNA, Tesla C2070

January 30, 2013 by hgpu

Efficient Implementation of MrBayes on multi-GPU

Jie Bao, Hongju Xia, Jianfu Zhou, Xiaoguang Liu, Gang Wang

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Tags: Bayesian, Biology, CUDA, GPU cluster, nVidia, nVidia GeForce GTX 480, Package, Task scheduling

January 28, 2013 by hgpu

The effects of nutrient chemotaxis on bacterial aggregation patterns with non-linear degenerate cross diffusion

J. Francisco Leyva, Carlos Malaga, Ramon G. Plaza

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Tags: Biological Physics, Biology, CUDA, Numerical simulation, nVidia, Tesla C2070

January 23, 2013 by hgpu

Burrows-Wheeler Aligner: A Parallel Approach

Sheridan Lee Wright

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Tags: Algorithms, Bioinformatics, Biology, CUDA, MPI, nVidia, Sequence alignment, Thesis

January 16, 2013 by hgpu

Acceleration of Selective Cationic Antibacterial Peptides computation: A comparison of FPGA and GPU approaches

D. Garcia-Ordaz, M. Arias-Estrada, M. Nuno-Maganda, C. Polanco, G. Del Rio

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Tags: Bioinformatics, Biology, CUDA, FPGA, nVidia, nVidia GeForce GT 230 M, nVidia GeForce GTX 480, Tesla M2070

January 13, 2013 by hgpu

Optimizations in Bioinformatics using GPU Processing on Binary Data

Manuel Belmadani

Tags: Algorithms, Bioinformatics, Biology, CUDA, nVidia, nVidia GeForce GTX 285

January 8, 2013 by hgpu

GPU-Optimized Coarse-Grained MD Simulations of Protein and RNA Folding and Assembly

Andrew J. Proctor, Tyson J. Lipscomb, Anqi Zou, Joshua A. Anderson, Samuel S. Cho

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Tags: Bioinformatics, Biology, CUDA, Macromolecule, Molecular dynamics, nVidia, RNA, Tesla C2070

January 8, 2013 by hgpu

Long Timestep Molecular Dynamics on the Graphical Processing Unit

James C. Sweet, Ronald J. Nowling, Trevor Cickovski, Christopher R. Sweet, Vijay S. Pande, Jesus A. Izaguirre

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Tags: Biology, Chemistry, CUDA, Molecular dynamics, nVidia, nVidia GeForce GTX 580, OpenCL, Package

January 4, 2013 by hgpu

High performance bioinformatics and computational biology on general-purpose graphics processing units

Cheng Ling

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Tags: Bioinformatics, Biology, Computational biology, CUDA, FPGA, nVidia, nVidia GeForce 8800 GTX, nVidia GeForce GTX 460, Sequence alignment, Thesis

January 3, 2013 by hgpu

Radionuclides migration modelling using artificial neural networks and parallel computing

O.S. Hilko, S.P. Kundas, I.A. Gishkeluk

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Tags: Algorithms, Biology, CUDA, MPI, Neural networks, nVidia, nVidia GeForce 9500 GT, nVidia GeForce 9800 GT, nVidia GeForce GT 220 M

December 29, 2012 by hgpu

Bioinformatics Sequence Comparisons on Manycore Processors

Tuan Tu Tran

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Tags: ATI, ATI Radeon HD 5870, Bioinformatics, Biology, nVidia, nVidia GeForce GTX 480, OpenCL, Review, Sequence matching, Thesis

December 25, 2012 by hgpu

Efficient reconstruction of biological networks via transitive reduction on general purpose graphics processors

Dragan Bosnacki, Maximilian R Odenbrett, Anton Wijs, Willem Ligtenberg, Peter Hilbers

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Tags: Algorithms, Bioinformatics, Biology, CUDA, nVidia, nVidia GeForce GTX 480, Package

November 23, 2012 by hgpu

Over-synchronization in GPU Programs

profile_util: simple C++ library to report memory, timing, thread affinity

Profile Util library: A quick and easy way to get MPI, OpenMP and GPU runtime information

MaC: Mamba CPU performance predictor

MambaCPU: Enhanced Correlation Mining with State Space Models for CPU Performance Prediction

Mixed-precision finite element kernels

Mixed-precision finite element kernels and assembly: Rounding error analysis and hardware acceleration

SHMT: The Simultaneous and Heterogenous Multithreading project

General-Purpose Computing on Tensor Processors

Superpipeline: A Universal Approach for Reducing GPU Memory Usage in Large Models

EnergyUCB-Bandit

Online Energy Optimization in GPUs: A Multi-Armed Bandit Approach

See all packages

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high performance computing on graphics processing units: hgpu.org

Faster Algorithms for RNA-folding using the Four-Russians method

Efficient Implementation of MrBayes on multi-GPU

The effects of nutrient chemotaxis on bacterial aggregation patterns with non-linear degenerate cross diffusion

Burrows-Wheeler Aligner: A Parallel Approach

Acceleration of Selective Cationic Antibacterial Peptides computation: A comparison of FPGA and GPU approaches

Optimizations in Bioinformatics using GPU Processing on Binary Data

GPU-Optimized Coarse-Grained MD Simulations of Protein and RNA Folding and Assembly

Long Timestep Molecular Dynamics on the Graphical Processing Unit

High performance bioinformatics and computational biology on general-purpose graphics processing units

Radionuclides migration modelling using artificial neural networks and parallel computing

Bioinformatics Sequence Comparisons on Manycore Processors

Efficient reconstruction of biological networks via transitive reduction on general purpose graphics processors

Recent source codes

Kokkidio: Kokkos+Eigen - write fast, readable multi-platform code

LLaMA-Inference-Bench

MATAR

Over-synchronization in GPU Programs

profile_util: simple C++ library to report memory, timing, thread affinity

MaC: Mamba CPU performance predictor

Mixed-precision finite element kernels

SHMT: The Simultaneous and Heterogenous Multithreading project

Superpipeline: A Universal Approach for Reducing GPU Memory Usage in Large Models

EnergyUCB-Bandit

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