high performance computing on graphics processing units: hgpu.org

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hgpu.org » Applications » Biology

Exploiting parallel features of modern computer architectures in bioinformatics: applications to genetics, structure comparison and large graph analysis

Guillaume Chapuis

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Tags: Algorithms, Bioinformatics, Biology, CUDA, Genetics, Graph theory, nVidia, Path problems, Tesla C2050, Thesis

July 3, 2014 by hgpu

Parallelizing the cellular potts model on GPU and multi-core CPU: An OpenCL cross-platform study

Chao Yu, Bo Yang

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Tags: ATI, ATI Radeon HD 7870, Biology, Computer science, OpenCL

July 1, 2014 by hgpu

Various String Matching Algorithms for DNA Sequences to Detect Breast Cancer using CUDA Processors

Nagaveni V, G T Raju

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Tags: Algorithms, Bioinformatics, Biology, CUDA, Databases, Medicine, nVidia, String matching, Tesla C2070

June 28, 2014 by hgpu

An efficient parallel algorithm for accelerating computational protein design

Yichao Zhou, Wei Xu, Bruce R. Donald, Jianyang Zeng

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Tags: Algorithms, Bioinformatics, Biology, CUDA, Java, nVidia, Package, Tesla K20

June 23, 2014 by hgpu

Fast Sequence Alignment Method Using CUDA-enabled GPU

Yeim-Kuan Chang, De-Yu Chen

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Tags: Bioinformatics, Biology, CUDA, nVidia, Sequence alignment, Smith-Waterman algorithm, Tesla C1060

June 19, 2014 by hgpu

GPU-accelerated Computation for Statistical Analysis of the Next-Generation Sequencing Data

Yilan Liu

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Tags: Bioinformatics, Biology, Computer science, CUDA, Next-Generation sequencing, nVidia, nVidia GeForce GTX 770

June 13, 2014 by hgpu

GPU-Accelerated Dynamic Functional Connectivity Analysis for Functional MRI Data Using OpenCL

D. Akgün, Ü. Sakoğlu, M. Mete, J. Esquivel, B. Adinoff

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Tags: Biology, Magnetic resonance imaging, Medicine, MRI, Neuroscience, nVidia, nVidia GeForce GTX 660, OpenCL

June 9, 2014 by hgpu

Massive exploration of perturbed conditions of the blood coagulation cascade through GPU parallelization

Paolo Cazzaniga, Marco S. Nobile, Daniela Besozzi, Matteo Bellini, Giancarlo Mauri

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Tags: Bioinformatics, Biology, Computational biology, CUDA, Differential equations, nVidia, ODEs, Ordinary differential equations, Tesla K20

May 30, 2014 by hgpu

Performance Evaluation of Quicksort with GPU Dynamic Parallelism for Gene-Expression Quantile Normalization

Roberto Pinto Souto, Carla Osthoff, Douglas Augusto, Oswaldo Trelles, Ana Tereza Ribeiro de Vasconcelos

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Tags: Algorithms, Bioinformatics, Biology, CUDA, nVidia, Sorting, Tesla K20

May 29, 2014 by hgpu

GPU-BSM: A GPU-Based Tool to Map Bisulfite-Treated Reads

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

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Tags: Bioinformatics, Biology, CUDA, Genetics, nVidia, nVidia GeForce GTX 480, Package, Python, Sequence alignment, Tesla K10, Tesla K20

May 25, 2014 by hgpu

Graphic Processing Unit Simulation of Axon Growth and Guidance through Cue Diffusion on Massively Parallel Processors

Ana M. Mihut, Graham Morgan, Marcus Kaiser

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Tags: Biology, CUDA, GLSL, Neuroscience, nVidia, nVidia GeForce GTX 460, nVidia Quadro 600, OpenGL, Programming techniques, Tesla K20

May 24, 2014 by hgpu

cuBLASTP: Fine-Grained Parallelization of Protein Sequence Search on a GPU

Jing Zhang, Hao Wang, Heshan Lin, Wu-chun Feng

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Tags: Bioinformatics, Biology, CUDA, Next-Generation sequencing, nVidia, Sequence alignment, Tesla K20

May 23, 2014 by hgpu

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BLOCKBENCH: A Framework for Analyzing Private Blockchains

Blockchain Goes Green? Part II: Characterizing the Performance and Cost of Blockchains on the Cloud and at the Edge

hls4ml: Machine learning on FPGAs using HLS

Real-time semantic segmentation on FPGAs for autonomous vehicles with hls4ml

AnySeq/GPU: A Novel Approach for Faster Sequence Alignment on GPUs

GPJSON: GPU-based JSON data processing system accessible via all GraalVM languages

GPU-based JSON data processing using structural indexes

NEPTUNE: Network- and GPU-aware management of serverless functions at the edge

NEPTUNE: Network- and GPU-aware Management of Serverless Functions at the Edge

HeCBench: a collection of Heterogeneous Computing benchmarks written with CUDA, HIP, SYCL (DPC++), and OpenMP-4.5

Experience of Migrating a Parallel Graph Coloring Program from CUDA to SYCL

cuPSO: GPU Parallelization for Particle Swarm Optimization Algorithms

WARPSPEED: An analytic Data Volume and Performance Estimator for GPU Kernels

Analytical Performance Estimation during Code Generation on Modern GPUs

Celerity HLA: A high-level API on top of Celerity to support functional, C++20 range-adaptors-like patterns

The Celerity High-level API: C++20 for Accelerator Clusters

GPU-Sched

CASE: A Compiler-Assisted SchEduling Framework for Multi-GPU Systems

See all packages

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high performance computing on graphics processing units: hgpu.org

Applications

Exploiting parallel features of modern computer architectures in bioinformatics: applications to genetics, structure comparison and large graph analysis

Parallelizing the cellular potts model on GPU and multi-core CPU: An OpenCL cross-platform study

Various String Matching Algorithms for DNA Sequences to Detect Breast Cancer using CUDA Processors

An efficient parallel algorithm for accelerating computational protein design

Fast Sequence Alignment Method Using CUDA-enabled GPU

GPU-accelerated Computation for Statistical Analysis of the Next-Generation Sequencing Data

GPU-Accelerated Dynamic Functional Connectivity Analysis for Functional MRI Data Using OpenCL

Massive exploration of perturbed conditions of the blood coagulation cascade through GPU parallelization

Performance Evaluation of Quicksort with GPU Dynamic Parallelism for Gene-Expression Quantile Normalization

GPU-BSM: A GPU-Based Tool to Map Bisulfite-Treated Reads

Graphic Processing Unit Simulation of Axon Growth and Guidance through Cue Diffusion on Massively Parallel Processors

cuBLASTP: Fine-Grained Parallelization of Protein Sequence Search on a GPU

Recent source codes

BLOCKBENCH: A Framework for Analyzing Private Blockchains

hls4ml: Machine learning on FPGAs using HLS

AnySeq/GPU: A Novel Approach for Faster Sequence Alignment on GPUs

GPJSON: GPU-based JSON data processing system accessible via all GraalVM languages

NEPTUNE: Network- and GPU-aware management of serverless functions at the edge

HeCBench: a collection of Heterogeneous Computing benchmarks written with CUDA, HIP, SYCL (DPC++), and OpenMP-4.5

cuPSO: GPU Parallelization for Particle Swarm Optimization Algorithms

WARPSPEED: An analytic Data Volume and Performance Estimator for GPU Kernels

Celerity HLA: A high-level API on top of Celerity to support functional, C++20 range-adaptors-like patterns

GPU-Sched

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