high performance computing on graphics processing units: hgpu.org

Applications

hgpu.org » Applications » Biology

A Hybrid Computational Grid Architecture for Comparative Genomics

A. Singh, Chen Chen, Weiguo Liu, W. Mitchell, B. Schmidt

Tags: Bioinformatics, Biology, Genetics, Sequence alignment

April 6, 2011 by hgpu

Enabling Energy-Efficient Analysis of Massive Neural Signals Using GPGPU

Dan Chen, Lizhe Wang, Shuaiting Wang, Muzhou Xiong, Gregor von Laszewski, Xiaoli Li

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Tags: Biology, CUDA, Medicine, Neuroscience, nVidia, nVidia GeForce GTX 295, Signal processing

April 5, 2011 by hgpu

GPGPU-Aided Ensemble Empirical-Mode Decomposition for EEG Analysis During Anesthesia

Dan Chen, Duan Li, Muzhou Xiong, Hong Bao, Xiaoli Li

Tags: Biology, Medicine, Signal processing

April 5, 2011 by hgpu

Neuromorphic models on a GPGPU cluster

Bing Han, T.M. Taha

Tags: Biology, GPU cluster, MPI, Neuroscience, nVidia, Tesla S1070

April 5, 2011 by hgpu

GPGPU implementation of a synaptically optimized, anatomically accurate spiking network simulator

Ruggero Scorcioni

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Tags: Biology, CUDA, Neuroscience, nVidia

April 4, 2011 by hgpu

The optimization of parallel Smith-Waterman sequence alignment using on-chip memory of GPGPU

Qian Zhang, Hong An, Gu Liu, Wenting Han, Ping Yao, Mu Xu, Xiaoqiang Li

Tags: Bioinformatics, Biology, CUDA, nVidia, Sequence alignment, Smith-Waterman algorithm

April 4, 2011 by hgpu

Poster: GPU-accelerated rigid body fitting of atomic structures into electron density maps

Edward W. Lowe Jr., Nils Woetzel, Jens Meiler

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Source codes

Tags: ATI, ATI Radeon HD 5970, Biology, Cryo-EM, Molecular modeling, nVidia, nVidia GeForce GTX 470, OpenCL, Package, Poster, Tesla C1060, Tesla C2050

April 1, 2011 by hgpu

Poster: GPU-accelerated artificial neural network for QSAR modeling

Edward W. Lowe Jr., Nils Woetzel, Jens Meiler

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Tags: ATI, ATI Radeon HD 5970, Biology, Neural networks, nVidia, nVidia GeForce GTX 470, OpenCL, Poster, Tesla C1060, Tesla C2050

April 1, 2011 by hgpu

Optimizing Smith-Waterman algorithm on Graphics Processing Unit

A. Khalafallah, H.F. Elbabb, O. Mahmoud, A. Elshamy

Tags: Bioinformatics, Biology, OpenCL, Sequence alignment, Smith-Waterman algorithm

April 1, 2011 by hgpu

Implementation of Smith-Waterman Algorithm in OpenCL for GPUs

Dzmitry Razmyslovich, Guillermo Marcus, Markus Gipp, Marc Zapatka, Andreas Szillus

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Tags: Bioinformatics, Biology, CUDA, nVidia, nVidia GeForce GTX 260, nVidia GeForce GTX 480, OpenCL, Poster, Sequence alignment, Smith-Waterman algorithm

March 31, 2011 by hgpu

CuHMMer: A load-balanced CPU-GPU cooperative bioinformatics application

Ping Yao, Hong An, Mu Xu, Gu Liu, Xiaoqiang Li, Yaobin Wang, Wenting Han

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Tags: Bioinformatics, Biology, CUDA, nVidia, nVidia GeForce 8800 GTX, Pattern Search

March 29, 2011 by hgpu

A GPU Implementation of Fast Parallel Markov Clustering in Bioinformatics Using EllPACK-R Sparse Data Format

A. Bustamam, K. Burrage, N.A. Hamilton

Tags: Bioinformatics, Biology, CUDA, nVidia

March 25, 2011 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

A Hybrid Computational Grid Architecture for Comparative Genomics

Enabling Energy-Efficient Analysis of Massive Neural Signals Using GPGPU

GPGPU-Aided Ensemble Empirical-Mode Decomposition for EEG Analysis During Anesthesia

Neuromorphic models on a GPGPU cluster

GPGPU implementation of a synaptically optimized, anatomically accurate spiking network simulator

The optimization of parallel Smith-Waterman sequence alignment using on-chip memory of GPGPU

Poster: GPU-accelerated rigid body fitting of atomic structures into electron density maps

Poster: GPU-accelerated artificial neural network for QSAR modeling

Optimizing Smith-Waterman algorithm on Graphics Processing Unit

Implementation of Smith-Waterman Algorithm in OpenCL for GPUs

CuHMMer: A load-balanced CPU-GPU cooperative bioinformatics application

A GPU Implementation of Fast Parallel Markov Clustering in Bioinformatics Using EllPACK-R Sparse Data Format

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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