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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

Real-Time Non-rigid Registration of Medical Images on a Cooperative Parallel Architecture

Yixun Liu, Andriy Fedorov, Ron Kikinis, Nikos Chrisochoides

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Tags: Bioinformatics, CUDA, Image registration, Medicine, nVidia, nVidia GeForce 8800 GT

January 17, 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

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

FPGA acceleration of the phylogenetic likelihood function for Bayesian MCMC inference methods

Stephanie Zierke, Jason Bakos

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Tags: Bioinformatics, Biology, FPGA

January 7, 2011 by hgpu

SeedFold: Scaling Biomolecular Structure Prediction

Tilus: A Tile-Level GPU Kernel Programming Language

Tilus: A Tile-Level GPGPU Programming Language for Low-Precision Computation

Memory-Efficient Acceleration of Block Low-Rank Foundation Models on Resource Constrained GPUs

CUDA-L2: Surpassing cuBLAS Performance for Matrix Multiplication through Reinforcement Learning

BoltzGen:Toward Universal Binder Design

cuPilot: A Strategy-Coordinated Multi-agent Framework for CUDA Kernel Evolution

MATLAB Tensor Core models

Accurate Models of NVIDIA Tensor Cores

TritonForge: Transform PyTorch Operations into Optimized GPU Kernels with LLMs

TritonForge: Profiling-Guided Framework for Automated Triton Kernel Optimization

RLTune: Hybrid Learning and Optimization-Based Dynamic Scheduling for DL Workloads on Heterogeneous GPU Clusters

Hybrid Learning and Optimization-Based Dynamic Scheduling for DL Workloads on Heterogeneous GPU Clusters

tritonBLAS: A Lightweight Triton-based General Matrix Multiplication (GEMM) Library

tritonBLAS: Triton-based Analytical Approach for GEMM Kernel Parameter Selection

See all packages

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high performance computing on graphics processing units: hgpu.org

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

Real-Time Non-rigid Registration of Medical Images on a Cooperative Parallel Architecture

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

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

FPGA acceleration of the phylogenetic likelihood function for Bayesian MCMC inference methods

Recent source codes

SeedFold: Scaling Biomolecular Structure Prediction

Tilus: A Tile-Level GPU Kernel Programming Language

Memory-Efficient Acceleration of Block Low-Rank Foundation Models on Resource Constrained GPUs

CUDA-L2: Surpassing cuBLAS Performance for Matrix Multiplication through Reinforcement Learning

BoltzGen:Toward Universal Binder Design

cuPilot: A Strategy-Coordinated Multi-agent Framework for CUDA Kernel Evolution

MATLAB Tensor Core models

TritonForge: Transform PyTorch Operations into Optimized GPU Kernels with LLMs

RLTune: Hybrid Learning and Optimization-Based Dynamic Scheduling for DL Workloads on Heterogeneous GPU Clusters

tritonBLAS: A Lightweight Triton-based General Matrix Multiplication (GEMM) Library

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