high performance computing on graphics processing units: hgpu.org

Applications

Fast free-form deformation using graphics processing units

Marc Modat, Gerard R. Ridgway, Zeike A. Taylor, Manja Lehmann, Josephine Barnes, David J. Hawkes, Nick C. Fox, Sebastien Ourselin

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Tags: Biology, CUDA, Image processing, Medicine, nVidia, nVidia GeForce 8800 GTX, Package

November 17, 2010 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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Tags: Bioinformatics, Biology, CUDA, Genetics, nVidia, nVidia GeForce GTX 280, Package, RNA

November 17, 2010 by hgpu

SHEsisEpi, a GPU-enhanced genome-wide SNP-SNP interaction scanning algorithm, efficiently reveals the risk of genetic epistasis in bipolar disorder

Xiaohan Hu, Qiang Liu, Zhao Zhang, Zhiqiang Li, Shilin Wang, Lin He, Yongyong Shi

Tags: Bioinformatics, Biology, Genetics

November 17, 2010 by hgpu

Alignator: A GPU powered software package for robust fiducial-less alignment of cryo tilt-series

Daniel Castano-Diez, Margot Scheffer, Ashraf Al-Amoudi, Achilleas S. Frangakis

Tags: Biology, Cryo-electron tomography, Image alignment, Image processing

November 17, 2010 by hgpu

Fast Bio-Inspired Computation using a GPU-based Systemic Computer

Marjan Rouhipour, Peter J. Bentley, Hooman Shayani

Tags: Biology

November 16, 2010 by hgpu

A configurable simulation environment for the efficient simulation of large-scale spiking neural networks on graphics processors

Jayram Moorkanikara M. Nageswaran, Nikil Dutt, Jeffrey L. Krichmar, Alex Nicolau, Alexander V. Veidenbaum

Tags: Biology, Computer science, CUDA, Neural networks, nVidia, nVidia GeForce GTX 280, STDP

November 13, 2010 by hgpu

Fast recursive filters for simulating nonlinear dynamic systems

J. H. van Hateren

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Tags: Algorithms, Biology, Neurons and Cognition

November 13, 2010 by hgpu

A molecular docking system using CUDA

Youngtae Roh, Jun Lee, Sungjun Park, Jee I. Kim

Tags: Bioinformatics, Biology, Biophysics, Chemistry, Molecular dynamics

November 9, 2010 by hgpu

ABC-SysBio–approximate Bayesian computation in Python with GPU support

Juliane Liepe, Chris Barnes, Erika Cule, Kamil Erguler, Paul Kirk, Tina Toni, Michael P. H. Stumpf

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Tags: Bioinformatics, Biology, CUDA, nVidia, Package, Python

November 9, 2010 by hgpu

Monte Carlo randomization tests for large-scale abundance datasets on the GPU

John L. Van Hemert, Julie A. Dickerson

Tags: Bioinformatics, Biology, CUDA, Medicine, Metabolomics, Monte Carlo simulation, Next-Generation sequencing, nVidia

November 8, 2010 by hgpu

Parallel, distributed and GPU computing technologies in single-particle electron microscopy

M. Schmeisser, B. C. Heisen, M. Luettich, B. Busche, F. Hauer, T. Koske, K. H. Knauber, H. Stark

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Tags: Biology, Cg, Cluster computing, Electron microscopy, GLSL, MPI, nVidia, OpenGL, Physics

November 8, 2010 by hgpu

GPU-based Real-Time Soft Tissue Deformation with Cutting and Haptic Feedback

Hadrien Courtecuisse, Hoeryong Jung, Jeremie Allard, Christian Duriez, Doo Y. Lee, Stephane Cotin

Tags: Biology, Biomechanics, Finite element method, Medicine, Surgical simulation

November 8, 2010 by hgpu

Awesome LLM-Driven Kernel Generation

Towards Automated Kernel Generation in the Era of LLMs

PhysProver: Advancing Automatic Theorem Proving for Physics

ParaCodex: A Profiling-Guided Autonomous Coding Agent for Reliable Parallel Code Generation and Translation

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

BoltzGen:Toward Universal Binder Design

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

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

MATLAB Tensor Core models

Accurate Models of NVIDIA Tensor Cores

See all packages

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high performance computing on graphics processing units: hgpu.org

Applications

Fast free-form deformation using graphics processing units

permGPU: Using graphics processing units in RNA microarray association studies

SHEsisEpi, a GPU-enhanced genome-wide SNP-SNP interaction scanning algorithm, efficiently reveals the risk of genetic epistasis in bipolar disorder

Alignator: A GPU powered software package for robust fiducial-less alignment of cryo tilt-series

Fast Bio-Inspired Computation using a GPU-based Systemic Computer

A configurable simulation environment for the efficient simulation of large-scale spiking neural networks on graphics processors

Fast recursive filters for simulating nonlinear dynamic systems

A molecular docking system using CUDA

ABC-SysBio–approximate Bayesian computation in Python with GPU support

Monte Carlo randomization tests for large-scale abundance datasets on the GPU

Parallel, distributed and GPU computing technologies in single-particle electron microscopy

GPU-based Real-Time Soft Tissue Deformation with Cutting and Haptic Feedback

Recent source codes

Awesome LLM-Driven Kernel Generation

PhysProver: Advancing Automatic Theorem Proving for Physics

ParaCodex: A Profiling-Guided Autonomous Coding Agent for Reliable Parallel Code Generation and Translation

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

BoltzGen:Toward Universal Binder Design

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

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

MATLAB Tensor Core models

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