high performance computing on graphics processing units: hgpu.org

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hgpu.org » Applications » Biology

Two-Level Approach to Efficient Visualization of Protein Dynamics

Ove Daae Lampe, I. Viola, N. Reuter, H. Hauser

Tags: Bioinformatics, Biology, Molecular dynamics, Rendering, 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

Fine-grain Parallelism using Multi-core, Cell/BE, and GPU Systems

Frederico Pratas, Pedro Trancoso, Leonel Sousa, Alexandros Stamatakis, Guochun Shi, Volodymyr Kindratenko

Tags: Bioinformatics, Biology, Cell processor, CUDA, Molecular dynamics, nVidia

August 25, 2011 by hgpu

EpiGPU

Gibran Hemani, Athanasios Theocharidis, Wenhua Wei, Chris Haley

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Source codes

Tags: ATI, Biology, Genetics, nVidia, OpenCL

August 21, 2011 by hgpu

Visual Computing in Biology and Medicine: Interactive visual analysis of contrast-enhanced ultrasound data based on small neighborhood statistics

Paolo Angelelli, Kim Nylund, Odd Helge Gilja, Helwig Hauser

Tags: Biology, Medicine, OpenCL, Ultrasound, Visualization

August 21, 2011 by hgpu

FPGA acceleration of rigid-molecule docking codes

Bharat Sukhwani, Martin C. Herbordt

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Tags: Biology, Biomolecules, CUDA, FPGA, Molecular modeling, nVidia, Performance, Tesla C1060

August 15, 2011 by hgpu

Network-on-Chip Hardware Accelerators for Biological Sequence Alignment

Souradip Sarkar, Gaurav Ramesh Kulkarni, Partha Pratim Pande, Ananth Kalyanaraman

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Tags: Algorithms, Bioinformatics, Biology, FPGA, Sequence alignment

August 12, 2011 by hgpu

High-performance biocomputing for simulating the spread of contagion over large contact networks

Keith R. Bisset, Ashwin M. Aji, Madhav V. Marathe, Wu-chun Feng

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Tags: Biology, CUDA, GPU cluster, nVidia, Tesla S2050

August 12, 2011 by hgpu

Optimized Parallel Implementation of Gillespie’s First Reaction Method on Graphics Processing Units

Cristian Dittamo, Davide Cangelos

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Tags: Algorithms, Biochemistry, Biology, nVidia, nVidia GeForce 8600 M GS, Stochastic simulation

August 12, 2011 by hgpu

Hardware accelerators for biocomputing: A survey

Souradip Sarkar, Turbo Majumder, Ananth Kalyanaraman, Partha Pratim Pande

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Tags: Biology, Cell processor, CUDA, FPGA, Molecular dynamics, nVidia, nVidia GeForce 7800 GTX, Performance, Review, Sequence alignment

August 7, 2011 by hgpu

Accelerated simulation of spiking neural networks using GPUs

Andreas K. Fidjeland, Murray P. Shanahan

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Tags: Biology, CUDA, Neural networks, nVidia, Tesla C1060

August 6, 2011 by hgpu

Unifying stream based and reconfigurable computing to design application accelerators

Bruno Francisco, Frederico Pratas, Leonel Sousa

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Tags: Bioinformatics, Biology, Computer science, Data parallelism, FPGA, nVidia, nVidia GeForce GTX 285

August 2, 2011 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

Two-Level Approach to Efficient Visualization of Protein Dynamics

Rapid RNA Folding: Analysis and Acceleration of the Zuker Recurrence

Fine-grain Parallelism using Multi-core, Cell/BE, and GPU Systems

EpiGPU

Visual Computing in Biology and Medicine: Interactive visual analysis of contrast-enhanced ultrasound data based on small neighborhood statistics

FPGA acceleration of rigid-molecule docking codes

Network-on-Chip Hardware Accelerators for Biological Sequence Alignment

High-performance biocomputing for simulating the spread of contagion over large contact networks

Optimized Parallel Implementation of Gillespie’s First Reaction Method on Graphics Processing Units

Hardware accelerators for biocomputing: A survey

Accelerated simulation of spiking neural networks using GPUs

Unifying stream based and reconfigurable computing to design application accelerators

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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