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hgpu.org » Applications » Biology

Neural Decoding using a Parallel Sequential Monte Carlo method on Point Processes with Ensemble Effect

Kai Xu, Yiwen Wang, Fang Wang, Yuxi Liao, Qiaosheng Zhang, Hongbao Li, Xiaoxiang Zheng

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Tags: Algorithms, Biology, CUDA, nVidia, nVidia GeForce GT 730 M

April 25, 2014 by hgpu

Local Alignment Tool Based on Hadoop Framework and GPU Architecture

Che-Lun Hun, Guan-Jie Hua

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Tags: Biology, Cloud, CUDA, Hadoop, MapReduce, nVidia, nVidia GeForce GTS 480, Sequence alignment

April 19, 2014 by hgpu

Bayesian Neural Networks for Genetic Association Studies of Complex Disease

Andrew L. Beam, Alison Motsinger-Reif, Jon Doyle

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Tags: Bayesian, Biology, CUDA, Machine learning, Neural networks, nVidia, Package, Python

April 17, 2014 by hgpu

New Efficient Method To Solve Longest Overlap Region Problem For Noncoding DNA Sequence

Yukun Zhong, ZhiWei He, XianHong Wang, Liao Gang

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Tags: Algorithms, Bioinformatics, Biology, CUDA, nVidia, nVidia GeForce GT 610 M

April 16, 2014 by hgpu

A Way For Accelerating The DNA Sequence Reconstruction Problem By CUDA

Yukun Zhong, ZhiWei He, XianHong Wang, XiongBin Cao

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Tags: Algorithms, Bioinformatics, Biology, CUDA, nVidia, nVidia GeForce GT 610 M, Sorting

April 16, 2014 by hgpu

An efficient GPU acceptance-rejection algorithm for the selection of the next reaction to occur for Stochastic Simulation Algorithms

Neri Mickael, Denis Mestivier

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Tags: Algorithms, Biology, Computer science, CUDA, nVidia, Optimization, Stochastic simulation, Tesla K10, Tesla K20, Tesla M2075, Tesla M2090

April 4, 2014 by hgpu

Multicore and GPU Algorithms for Nussinov RNA Folding

J. Li, S. Ranka, S. Sahni

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Tags: Biology, CUDA, nVidia, nVidia Tesla C2050, RNA

April 3, 2014 by hgpu

Pairwise Sequence Alignment for Very Long Sequences on GPUs

J. Li, S. Ranka, S. Sahni

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Tags: CUDA, Genetics, nVidia, nVidia Tesla C2050, Sequence alignment, Smith-Waterman algorithm

April 2, 2014 by hgpu

Competing computational approaches to reaction-diffusion equations in clusters of cells

S. Stella, R. Chignola, E. Milotti

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Tags: Biology, CUDA, Diffusion equation, Medicine, nVidia, nVidia Quadro 4000, Partial differential equations, PDEs

March 19, 2014 by hgpu

MaxSSmap: A GPU program for short read mapping with the maximum scoring subsequence

Usman Roshan

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Tags: Bioinformatics, Biology, CUDA, nVidia, Short read mapping, Smith-Waterman algorithm, Tesla M2050

March 12, 2014 by hgpu

Parallelization of DNA alignment algorithms using GPUs

Gustavo Encarnacao

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Tags: Algorithms, Bioinformatics, Biology, CUDA, nVidia, nVidia GeForce GTX 580, Sequence matching, Suffix trees

March 7, 2014 by hgpu

Hybrid Framework for pairwise DNA Sequence Alignment Using the CUDA compatible GPU

H. Khaled, R. El Gohary, N.L. Badr, H. M. Faheem

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Tags: Bioinformatics, Biology, CUDA, nVidia, nVidia GeForce GT 540 M, Sequence alignment, Smith-Waterman algorithm

March 6, 2014 by hgpu

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Octo-Tiger: Astrophysics program simulating the evolution of star systems based on the fast multipole method on adaptive Octrees

Stellar Mergers with HPX-Kokkos and SYCL: Methods of using an Asynchronous Many-Task Runtime System with SYCL

BAT: A standardized benchmark suite for auto-tuners

Towards a Benchmarking Suite for Kernel Tuners

BenchDirect: A Directed Language Model for Compiler Benchmarks

A Deep Learning Model for Loop Interchange

Bridging Control-Centric and Data-Centric Optimization

Advanced evolutionary computation library built directly on top of PyTorch, created at NNAISENSE

EvoTorch: Scalable Evolutionary Computation in Python

See all packages

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high performance computing on graphics processing units: hgpu.org

Applications

Neural Decoding using a Parallel Sequential Monte Carlo method on Point Processes with Ensemble Effect

Bayesian Neural Networks for Genetic Association Studies of Complex Disease

New Efficient Method To Solve Longest Overlap Region Problem For Noncoding DNA Sequence

A Way For Accelerating The DNA Sequence Reconstruction Problem By CUDA

An efficient GPU acceptance-rejection algorithm for the selection of the next reaction to occur for Stochastic Simulation Algorithms

Multicore and GPU Algorithms for Nussinov RNA Folding

Pairwise Sequence Alignment for Very Long Sequences on GPUs

Competing computational approaches to reaction-diffusion equations in clusters of cells

MaxSSmap: A GPU program for short read mapping with the maximum scoring subsequence

Parallelization of DNA alignment algorithms using GPUs

Hybrid Framework for pairwise DNA Sequence Alignment Using the CUDA compatible GPU

Recent source codes

E2C-Sim: a simulator and workload generator for Edge-to-Cloud environments

Kernel Tuner

Clava: C/C++ Source-to-Source Tool based on Clang

gpuLik

Octo-Tiger: Astrophysics program simulating the evolution of star systems based on the fast multipole method on adaptive Octrees

BAT: A standardized benchmark suite for auto-tuners

BenchDirect: A Directed Language Model for Compiler Benchmarks

A Deep Learning Model for Loop Interchange

Bridging Control-Centric and Data-Centric Optimization

Advanced evolutionary computation library built directly on top of PyTorch, created at NNAISENSE

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