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Efficient Bayesian inference in stochastic chemical kinetic models using graphical processing units

Jarad Niemi, Matthew Wheeler

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Tags: Bayesian, Biology, Chemistry, CUDA, nVidia, Stochastic simulation, Tesla T10

January 26, 2011 by hgpu

Energy efficient biomolecular simulations with FPGA-based reconfigurable computing

Ananth Nallamuthu, Melissa C. Smith, Scott Hampton, Pratul K. Agarwal, Sadaf R. Alam

Tags: Bioinformatics, Biology, FPGA, Molecular dynamics

January 19, 2011 by hgpu

Towards microsecond biological molecular dynamics simulations on hybrid processors

Scott Hampton, Pratul K. Agarwal, Sadaf R. Alam, Paul S. Crozier

Tags: Bioinformatics, Biology, CUDA, Molecular dynamics, nVidia, Tesla C1060, Tesla C2050

January 19, 2011 by hgpu

Optimal Utilization of Heterogeneous Resources for Biomolecular Simulations

Scott S. Hampton, Sadaf R. Alam, Paul S. Crozier, Pratul K. Agarwal

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Tags: Bioinformatics, Biology, CUDA, Molecular dynamics, nVidia, Tesla C1060, Tesla C2050

January 19, 2011 by hgpu

Fast Genetic Programming on GPUs

Simon Harding, Wolfgang Banzhaf

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Tags: Bioinformatics, Biology, DirectX, Genetics, nVidia, nVidia GeForce 7300

January 15, 2011 by hgpu

GPU accelerated biochemical network simulation

Yanxiang Zhou, Juliane Liepe, Xia Sheng, Michael P. H. Stumpf, Chris Barnes

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Tags: Bioinformatics, Biology, CUDA, GPU cluster, nVidia, Package, Tesla C2050

January 13, 2011 by hgpu

Rapid evaluation and evolution of neural models using graphics card hardware

Thomas F. Clayton, Leena N. Patel, Gareth Leng, Alan F. Murray, Iain A.B. Lindsay

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Tags: Algorithms, Bioinformatics, Biology, CUDA, Evolutionary Computations, nVidia, nVidia GeForce 8800 GTX

January 13, 2011 by hgpu

Automated image alignment for 2D gel electrophoresis in a high-throughput proteomics pipeline

Andrew W. Dowsey, Michael J. Dunn, Guang-Zhong Z. Yang

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Tags: Bioinformatics, Biology, Cg, Image alignment, nVidia, nVidia GeForce 6800 Ultra, Package

January 11, 2011 by hgpu

SCELib3.0: The new revision of SCELib, the parallel computational library of molecular properties in the Single Center Approach

N. Sanna, I. Baccarelli, G. Morelli

Tags: Biology, Chemistry, CUDA, Molecular modeling, nVidia

January 11, 2011 by hgpu

Fast binding site mapping using GPUs and CUDA

Bharat Sukhwani, Martin C. Herbordt

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Tags: Bioinformatics, Biology, CUDA, Molecular dynamics, nVidia, Tesla C1060

January 11, 2011 by hgpu

Quality-score guided error correction for short-read sequencing data using CUDA

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

Tags: Bioinformatics, Biology, CUDA, Error recovery, Genetics, nVidia

January 11, 2011 by hgpu

CBESW: sequence alignment on the Playstation 3

Adrianto Wirawan, Chee Keong K. Kwoh, Nim Tri T. Hieu, Bertil Schmidt

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Tags: Algorithms, Bioinformatics, Biology, BLAST, Cell processor, CUDA, nVidia, nVidia GeForce 8800 GTX, Package, Playstation, Sequence alignment, Smith-Waterman algorithm

January 8, 2011 by hgpu

Specx: Speculative task-based runtime system

Specx: a C++ task-based runtime system for heterogeneous distributed architectures

Mutual-Supervised Learning for Sequential-to-Parallel Code Translation

KISim: Kubernetes Intelligent Scheduling Simulator

KIS-S: A GPU-Aware Kubernetes Inference Simulator with RL-Based Auto-Scaling

Hardware Compute Partitioning on NVIDIA GPUs for Composable Systems

Efficient GPU Implementation of Multi-Precision Integer Division

ParEval: A Parallel Code Evaluation Benchmark

ParEval-Repo: A Benchmark Suite for Evaluating LLMs with Repository-level HPC Translation Tasks

FlashSparse: Minimizing Computation Redundancy for Fast Sparse Matrix Multiplications on Tensor Cores

Libra: Synergizing CUDA and Tensor Cores for High-Performance Sparse Matrix Multiplication

exa-AMD: Exascale Accelerated Materials Discovery

Accelerated discovery and design of Fe-Co-Zr magnets with tunable magnetic anisotropy through machine learning and parallel computing

WiLLM: An Open Wireless LLM Communication System

Vcc: the Vulkan Clang Compiler

No More Shading Languages: Compiling C++ to Vulkan Shaders

See all packages

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high performance computing on graphics processing units: hgpu.org

Applications

Efficient Bayesian inference in stochastic chemical kinetic models using graphical processing units

Energy efficient biomolecular simulations with FPGA-based reconfigurable computing

Towards microsecond biological molecular dynamics simulations on hybrid processors

Optimal Utilization of Heterogeneous Resources for Biomolecular Simulations

Fast Genetic Programming on GPUs

GPU accelerated biochemical network simulation

Rapid evaluation and evolution of neural models using graphics card hardware

Automated image alignment for 2D gel electrophoresis in a high-throughput proteomics pipeline

SCELib3.0: The new revision of SCELib, the parallel computational library of molecular properties in the Single Center Approach

Fast binding site mapping using GPUs and CUDA

Quality-score guided error correction for short-read sequencing data using CUDA

CBESW: sequence alignment on the Playstation 3

Recent source codes

Specx: Speculative task-based runtime system

Mutual-Supervised Learning for Sequential-to-Parallel Code Translation

KISim: Kubernetes Intelligent Scheduling Simulator

Hardware Compute Partitioning on NVIDIA GPUs for Composable Systems

Efficient GPU Implementation of Multi-Precision Integer Division

ParEval: A Parallel Code Evaluation Benchmark

FlashSparse: Minimizing Computation Redundancy for Fast Sparse Matrix Multiplications on Tensor Cores

exa-AMD: Exascale Accelerated Materials Discovery

WiLLM: An Open Wireless LLM Communication System

Vcc: the Vulkan Clang Compiler

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