high performance computing on graphics processing units: hgpu.org

hgpu.org » RNA

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

Parallelization of Data Intensive Code Using Computer Unified Device Architecture (CUDA)

Bhardwaj Aditi, Bhardwaj Rohatash K., Shishir K. Gangwar

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Tags: Algorithms, Biology, CUDA, nVidia, RNA

July 26, 2012 by hgpu

GPU-Optimized Molecular Dynamics Simulations

Tyson J. Lipscomb

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Tags: Biology, Biomolecules, CUDA, Molecular dynamics, nVidia, nVidia GeForce GTX 480, nVidia GeForce GTX 580, Optimization, Pseudo-random number generators, Review, RNA, Tesla C2070, Thesis

July 8, 2012 by hgpu

CPU-GPU hybrid accelerating the Zuker algorithm for RNA secondary structure prediction application

Guoqing Lei, Yong Dou, Wen Wan, Fei Xia, Rongchun Li, Meng Ma, Dan Zou

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Tags: Algorithms, Bioinformatics, Biology, CUDA, Hybrid computing, nVidia, nVidia GeForce GTX 580, RNA

January 15, 2012 by hgpu

Manycore high-performance computing in bioinformatics

Jean-Stephane Varre, Bertil Schmidt, Stephane Janot, Mathieu Giraud

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Tags: Algorithms, Bioinformatics, Biology, CUDA, nVidia, OpenCL, Review, RNA, Sequence alignment

September 26, 2011 by hgpu

Accelerating popular tomographic reconstruction algorithms on commodity PC graphics hardware

Fang Xu, K. Mueller

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Tags: Algorithms, Computed tomography, CT, Image reconstruction, Medicine, nVidia, nVidia GeForce FX 5900, RNA, Visualization

August 31, 2011 by hgpu

Rapid RNA Folding: Analysis and Acceleration of the Zuker Recurrence

Arpith C. Jacob, Jeremy D. Buhler, Roger D. Chamberlain

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Tags: Algorithms, Bioinformatics, Biology, Computational biology, CUDA, FPGA, nVidia, nVidia GeForce GTX 280, RNA, Tesla C870

August 27, 2011 by hgpu

Single molecule detection of tuberculosis nucleic acid using dark field Tethered Particle Motion

Sanneke Brinkers, Heidelinde R.C. Dietrich, Sjoerd Stallinga, Jurriaan J. Mes, Ian T. Young, Bernd Rieger

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Tags: Algorithms, Biology, Biophysics, RNA

June 9, 2011 by hgpu

permGPU: Using graphics processing units in RNA microarray association studies

Ivo Shterev, Sin H. Jung, Stephen George, Kouros Owzar

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Source codes

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

November 17, 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

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

Parallelization of Data Intensive Code Using Computer Unified Device Architecture (CUDA)

GPU-Optimized Molecular Dynamics Simulations

CPU-GPU hybrid accelerating the Zuker algorithm for RNA secondary structure prediction application

Manycore high-performance computing in bioinformatics

Accelerating popular tomographic reconstruction algorithms on commodity PC graphics hardware

Rapid RNA Folding: Analysis and Acceleration of the Zuker Recurrence

Single molecule detection of tuberculosis nucleic acid using dark field Tethered Particle Motion

permGPU: Using graphics processing units in RNA microarray association studies

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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