high performance computing on graphics processing units: hgpu.org

Applications

hgpu.org » Applications » Biology

MICA: A fast short-read aligner that takes full advantage of Intel Many Integrated Core Architecture (MIC)

Sze-Hang Chan, Jeanno Cheung, Edward Wu, Heng Wang, Chi-Man Liu, Xiaoqian Zhu, Shaoliang Peng, Ruibang Luo, Tak-Wah Lam

View

Download (PDF)

Source codes

Tags: Bioinformatics, Biology, Intel Xeon Phi, Package

February 21, 2014 by hgpu

Parallel implementation of 3D protein structure similarity searches using a GPU and the CUDA

Dariusz Mrozek, Milosz Brozek, Bozena Malysiak-Mrozek

View

Download (PDF)

Source codes

Tags: Algorithms, Bioinformatics, Biology, CUDA, nVidia, nVidia GeForce GTX 285, nVidia GeForce GTX 560 Ti, Package, Tesla C1060

February 4, 2014 by hgpu

A tool for mapping Single Nucleotide Polymorphisms using Graphics Processing Units

Andrea Manconi, Alessandro Orro, Emanuele Manca, Giuliano Armano, Luciano Milanesi

View

Download (PDF)

Tags: Algorithms, Bioinformatics, Biology, CUDA, nVidia, nVidia GeForce GTX 480, Package, Smith-Waterman algorithm, Tesla K20

January 12, 2014 by hgpu

Nengo: a Python tool for building large-scale functional brain models

Trevor Bekolay, James Bergstra, Eric Hunsberger, Travis DeWolf, Terrence C. Stewart, Daniel Rasmussen, Xuan Choo, Aaron Russell Voelker, Chris Eliasmith

View

Download (PDF)

Source codes

Tags: ATI, ATI Radeon HD 7970, Biology, Neuroscience, nVidia, nVidia GeForce GTX 280, OpenCL, Package, PyOpenCL, Python

January 9, 2014 by hgpu

HUGO: Hierarchical mUlti-reference Genome cOmpression for aligned reads

Pinghao Li, Xiaoqian Jiang, Shuang Wang, Jihoon Kim, Hongkai Xiong, Lucila Ohno-Machado

View

Download (PDF)

Source codes

Tags: Algorithms, Bioinformatics, Biology, Clustering, Compression, CUDA, nVidia, Package, Sequence alignment, Tesla M2090

December 27, 2013 by hgpu

Neurokernel: An Open Scalable Software Framework for Emulation and Validation of Drosophila Brain Models on Multiple GPUs

Lev E. Givon, Aurel A. Lazar

View

Download (PDF)

Source codes

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

November 18, 2013 by hgpu

Accelerating calculations of RNA secondary structure partition functions using GPUs

Harry A Stern, David H Mathews

View

Download (PDF)

Source codes

Tags: Bioinformatics, Biology, CUDA, nVidia, Package, RNA, Tesla M2050

November 11, 2013 by hgpu

cudaMap: a GPU accelerated program for gene expression connectivity mapping

Darragh G McArt, Peter Bankhead, Philip D Dunne, Manuel Salto-Tellez, Peter Hamilton, Shu-Dong Zhang

View

Download (PDF)

Source codes

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

October 17, 2013 by hgpu

High performance sequence mining using pairwise statistical significance

Yuhong Zhang, Feng Chen

View

Download (PDF)

Source codes

Tags: Algorithms, Bioinformatics, Biology, CUDA, nVidia, Package, Tesla C2050

October 12, 2013 by hgpu

Improving Resource Utilization in Heterogeneous CPU-GPU Systems

Michael Boyer

View

Download (PDF)

Source codes

Tags: Algorithms, ATI, ATI Radeon HD 5870, ATI Radeon HD 7970, Biology, Computer science, CUDA, Heterogeneous systems, nVidia, nVidia GeForce GTX 280, OpenCL, Package, Software Engineering, Thesis

September 23, 2013 by hgpu

A Novel CPU/GPU Simulation Environment for Large-Scale Biologically-Realistic Neural Modeling

Roger V. Hoang, Devyani Tanna, Laurence C. Jayet Bray, Sergiu M. Dascalu, Frederick C. Harris Jr.

View

Download (PDF)

Source codes

Tags: Biology, CUDA, Neural networks, Neuroscience, nVidia, nVidia GeForce GTX 460, nVidia GeForce GTX 480, nVidia GeForce GTX 680, Package, Tesla C2050

September 14, 2013 by hgpu

GUESS-ing Polygenic Associations with Multiple Phenotypes Using a GPU-Based Evolutionary Stochastic Search Algorithm

Leonardo Bottolo, Marc Chadeau-Hyam, David I. Hastie, Tanja Zeller, Benoit Liquet, Paul Newcombe, Loic Yengo, Philipp S. Wild, Arne Schillert, Andreas Ziegler, Sune F. Nielsen, Adam S. Butterworth, Weang Kee Ho, Raphaele Castagne, Thomas Munzel, David Tregouet, Mario Falchi15, Francois Cambien, Borge G. Nordestgaard, Frederic Fumeron, Anne Tybjaerg-Hansen, Philippe Froguel, John Danesh, Enrico Petretto, Stefan Blankenberg, Laurence Tiret, Sylvia Richardson

View

Download (PDF)

Source codes

Tags: Algorithms, Bayesian, Bioinformatics, Biology, CUDA, nVidia, Package, Tesla C1060

August 16, 2013 by hgpu

* * *

high performance computing on graphics processing units: hgpu.org

Applications

MICA: A fast short-read aligner that takes full advantage of Intel Many Integrated Core Architecture (MIC)

Parallel implementation of 3D protein structure similarity searches using a GPU and the CUDA

A tool for mapping Single Nucleotide Polymorphisms using Graphics Processing Units

Nengo: a Python tool for building large-scale functional brain models

HUGO: Hierarchical mUlti-reference Genome cOmpression for aligned reads

Neurokernel: An Open Scalable Software Framework for Emulation and Validation of Drosophila Brain Models on Multiple GPUs

Accelerating calculations of RNA secondary structure partition functions using GPUs

cudaMap: a GPU accelerated program for gene expression connectivity mapping

High performance sequence mining using pairwise statistical significance

Improving Resource Utilization in Heterogeneous CPU-GPU Systems

A Novel CPU/GPU Simulation Environment for Large-Scale Biologically-Realistic Neural Modeling

GUESS-ing Polygenic Associations with Multiple Phenotypes Using a GPU-Based Evolutionary Stochastic Search Algorithm

Recent source codes

torchPDLP: Primal-Dual Linear Programming in PyTorch. In collaboration with AMD and IPAM

Benchmarks for Dissecting CPU-GPU Unified Physical Memory on AMD MI300A APUs

kvcached: Elastic KV cache for dynamic GPU sharing and efficient multi-LLM inference

Bandicoot: C++ library for GPU accelerated linear algebra

Luthier: Bridging Auto-Tuning and Vendor Libraries for Efficient Deep Learning Inference

Fused Kernel Library (FKL)

GPUHammer: Rowhammer Attacks on GPU Memories are Practical

Block: Balance Loader of LLM Serving with Context, Knowledge and Predictive Scheduling

SIGMo: Scalable Isomorphism Graph Matching on GPUs

DGEMM without FP64 Arithmetic - using FP64 Emulation and FP8 Tensor Cores with Ozaki Scheme

Most viewed papers (last 30 days)