high performance computing on graphics processing units: hgpu.org

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hgpu.org » Applications » Biology

Parallel reconstruction of neighbor-joining trees for large multiple sequence alignments using CUDA

Yongchao Liu, Bertil Schmidt, Douglas L. Maskell

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Tags: Bioinformatics, Biology, CUDA, nVidia, nVidia GeForce GTX 280, Sequence alignment, Smith-Waterman algorithm

November 27, 2010 by hgpu

Implications of the Turing completeness of reaction-diffusion models, informed by GPGPU simulations on an XBox 360: cardiac arrhythmias, re-entry and the Halting problem

Simon Scarle

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Tags: Biology, Heart, Medicine, Visualization, Xbox 360

November 27, 2010 by hgpu

CUDA-MEME: Accelerating Motif Discovery in Biological Sequences Using CUDA-enabled Graphics Processing Units

Yongchao Liu, Bertil Schmidt, Weiguo Liu, Douglas L. Maskell

Tags: Biology, CUDA, nVidia, nVidia GeForce GTX 280, Pattern recognition

November 27, 2010 by hgpu

Performance Analysis of IBM Cell Broadband Engine on Sequence Alignment

Yang Song, Gregory M. Striemer, Ali Akoglu

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Tags: Bioinformatics, Biology, Cell processor, CUDA, nVidia, Sequence alignment, Smith-Waterman algorithm, Tesla C870

November 27, 2010 by hgpu

Accelerating leukocyte tracking using CUDA: A case study in leveraging manycore coprocessors

M. Boyer, D. Tarjan, S. T. Acton, K. Skadron

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Tags: Biology, CUDA, Microscopy, nVidia, nVidia GeForce GTX 280

November 26, 2010 by hgpu

Many-core algorithms for statistical phylogenetics

Marc A. Suchard, Andrew Rambaut

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Tags: Bioinformatics, Biology, CUDA, Genetics, nVidia, nVidia GeForce GTX 280

November 23, 2010 by hgpu

A Parallel Algorithm for Error Correction in High-Throughput Short-Read Data on CUDA-Enabled Graphics Hardware

Haixiang Shi, Bertil Schmidt, Weiguo Liu, Wolfgang Muller-Wittig

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Tags: Biology, Computer science, CUDA, Error recovery, nVidia, Package

November 22, 2010 by hgpu

Parallel Position Weight Matrices Algorithms

Mathieu Giraud, Jean-Stephane Varre

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Tags: Biology, Computer science, CUDA, nVidia, nVidia GeForce 8800, nVidia GeForce GTX 280, Package

November 22, 2010 by hgpu

MSA-CUDA: Multiple Sequence Alignment on Graphics Processing Units with CUDA

Yongchao Liu, Bertil Schmidt, Douglas L. Maskell

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Tags: Bioinformatics, Biology, CUDA, nVidia, nVidia GeForce GTX 280, Sequence alignment

November 21, 2010 by hgpu

Patient-Specific Non-Linear Finite Element Modelling for Predicting Soft Organ Deformation in Real-Time; Application to Non-Rigid Neuroimage Registration

Adam Wittek, Grand Joldes, Mathieu Couton, Simon K. Warfield, Karol Miller

Tags: Biology, Medicine, nVidia, Surgical simulation, Tesla C870

November 20, 2010 by hgpu

Ultra-fast FFT protein docking on graphics processors

David W. Ritchie, Vishwesh Venkatraman

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

November 19, 2010 by hgpu

Acceleration of the Smith-Waterman Algorithm using Single and Multiple Graphics Processors

Ali Khajeh-Saeed, Stephen Poole, J. Blair Perot

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Tags: Bioinformatics, Biology, CUDA, nVidia, nVidia GeForce 9800 GT, nVidia GeForce 9800 GTX, nVidia GeForce GTX 295, Sequence matching, Smith-Waterman algorithm

November 18, 2010 by hgpu

SimSYCL: Synchronous, single-threaded, library-only SYCL implementation for debugging and verification

SimSYCL: A SYCL Implementation Targeting Development, Debugging, Simulation and Conformance

gpu_tracker: Context manager and CLI that tracks the computational-resource-usage of a code block or shell command, particularly the GPU usage

gpu_tracker: Python package for tracking and profiling GPU utilization in both desktop and high-performance computing environments

CIFAR-10 Airbench: 94% on CIFAR-10 in 3.29 second

94% on CIFAR-10 in 3.29 Seconds on a Single GPU

LOOPer: a polyhedral compiler for expressing fast and portable data parallel algorithms

LOOPer: A Learned Automatic Code Optimizer For Polyhedral Compilers

OpenMC Monte Carlo Code

Performance Portable Monte Carlo Particle Transport on Intel, NVIDIA, and AMD GPUs

Polygeist: C/C++ frontend for MLIR

Retargeting and Respecializing GPU Workloads for Performance Portability

Parallel Gaussian process with kernel approximation in CUDA

See all packages

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high performance computing on graphics processing units: hgpu.org

Applications

Parallel reconstruction of neighbor-joining trees for large multiple sequence alignments using CUDA

Implications of the Turing completeness of reaction-diffusion models, informed by GPGPU simulations on an XBox 360: cardiac arrhythmias, re-entry and the Halting problem

CUDA-MEME: Accelerating Motif Discovery in Biological Sequences Using CUDA-enabled Graphics Processing Units

Performance Analysis of IBM Cell Broadband Engine on Sequence Alignment

Accelerating leukocyte tracking using CUDA: A case study in leveraging manycore coprocessors

Many-core algorithms for statistical phylogenetics

A Parallel Algorithm for Error Correction in High-Throughput Short-Read Data on CUDA-Enabled Graphics Hardware

Parallel Position Weight Matrices Algorithms

MSA-CUDA: Multiple Sequence Alignment on Graphics Processing Units with CUDA

Patient-Specific Non-Linear Finite Element Modelling for Predicting Soft Organ Deformation in Real-Time; Application to Non-Rigid Neuroimage Registration

Ultra-fast FFT protein docking on graphics processors

Acceleration of the Smith-Waterman Algorithm using Single and Multiple Graphics Processors

Recent source codes

SimSYCL: Synchronous, single-threaded, library-only SYCL implementation for debugging and verification

GPU plugin for PySCF

QArray

Celerity: High-level C++ for Accelerator Clusters

gpu_tracker: Context manager and CLI that tracks the computational-resource-usage of a code block or shell command, particularly the GPU usage

CIFAR-10 Airbench: 94% on CIFAR-10 in 3.29 second

LOOPer: a polyhedral compiler for expressing fast and portable data parallel algorithms

OpenMC Monte Carlo Code

Polygeist: C/C++ frontend for MLIR

Parallel Gaussian process with kernel approximation in CUDA

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