NMF-mGPU 1.0 – Non-negative Matrix Factorization on multi-GPU Systems

NMF-mGPU 1.0

:: DESCRIPTION

NMF-mGPU implements the Non-negative Matrix Factorization (NMF) algorithm by making use of Graphics Processing Units (GPUs).

::DEVELOPER

Biocomputing Unit – CNB

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux
  • CUDA Toolkit and CUDA Driver:

:: DOWNLOAD

 NMF-mGPU

:: MORE INFORMATION

Citation:

NMF-mGPU: non-negative matrix factorization on multi-GPU systems.
Mejía-Roa E, Tabas-Madrid D, Setoain J, García C, Tirado F, Pascual-Montano A.
BMC Bioinformatics. 2015 Feb 13;16:43. doi: 10.1186/s12859-015-0485-4.

BALSA 2.0 – GPU Accelerated Integrated WGS and WES Secondary Analysis

BALSA 2.0

:: DESCRIPTION

BALSA is an integrated solution for the secondary analysis of next generation sequencing data; it exploits the computational power of GPU and an intricate memory management to give a fast and accurate analysis.

::DEVELOPER

L3 Bioinformatics Limited

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux
  • GPU

:: DOWNLOAD

 BALSA

:: MORE INFORMATION

Citation

BALSA: integrated secondary analysis for whole-genome and whole-exome sequencing, accelerated by GPU.
Luo R, Wong YL, Law WC, Lee LK, Cheung J, Liu CM, Lam TW.
PeerJ. 2014 Jun 3;2:e421. doi: 10.7717/peerj.421.

GPU-BLAST 1.1 – Sequence Alignment with GPUs

GPU-BLAST 1.1

:: DESCRIPTION

GPU-BLAST is an accelerated version of the popular NCBI-BLAST using a general-purpose graphics processing unit (GPU). The implementation is based on the source code of NCBI-BLAST, thus maintaining the same input and output interface while producing identical results. In comparison to the sequential NCBI-BLAST, the speedups achieved by GPU-BLAST range mostly between 3 and 4.

::DEVELOPER

Panagiotis D. Vouzis and Nikolaos V. Sahinidis

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux
  • C++
  • CUDA

:: DOWNLOAD

GPU-BLAST

:: MORE INFORMATION

Citation

Panagiotis D. Vouzis and Nikolaos V. Sahinidis,
GPU-BLAST: using graphics processors to accelerate protein sequence alignment,”
Bioinformatics, 2011 Vol. 27, no. 2, pages 182-188,

QuickProbs 1.02 – Multiple Sequence Alignment designed especially for GPU

QuickProbs 1.02

:: DESCRIPTION

QuickProbs is a fast multiple sequence alignment algorithm designed for graphics processors.

::DEVELOPER

REFRESH Bioinformatics Group

:: SCREENSHOTS

n/a

:: REQUIREMENTS

  • Linux / Windows

:: DOWNLOAD

  QuickProbs

:: MORE INFORMATION

Citation

PLoS One. 2014 Feb 25;9(2):e88901. doi: 10.1371/journal.pone.0088901. eCollection 2014.
QuickProbs–a fast multiple sequence alignment algorithm designed for graphics processors.
Gudyś A, Deorowicz S

gPGA 1.0 – GPU Accelerated Population Genetics Analyses

gPGA 1.0

:: DESCRIPTION

gPGA (GPU Accelerated Population Genetics Analyses) is the extension of IM program that can effectively implement on Graphics Processing Unit (GPU).

::DEVELOPER

Chunbao Zhou (zhoucb@sccas.cn)

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux

:: DOWNLOAD

 gPGA

:: MORE INFORMATION

Citation

gPGA: GPU Accelerated Population Genetics Analyses.
Zhou C, Lang X, Wang Y, Zhu C.
PLoS One. 2015 Aug 6;10(8):e0135028. doi: 10.1371/journal.pone.0135028. eCollection 2015.

GPUmotif – GPU-accelerated ultra-fast and Energy-efficient Motif analysis

GPUmotif

:: DESCRIPTION

GPUmotif is a GPU-accelerated ultra-fast and energy-efficient motif analysis program.

::DEVELOPER

GPUmotif team

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux
  • NVIDIA graphics cards

:: DOWNLOAD

 GPUmotif

:: MORE INFORMATION

Citation

GPUmotif: an ultra-fast and energy-efficient motif analysis program using graphics processing units.
Zandevakili P, Hu M, Qin Z.
PLoS One. 2012;7(5):e36865. doi: 10.1371/journal.pone.0036865.

TSP/TST (GPU) 1.1 – Top-Scoring Pair and Top-Scoring Triple on the GPU

TSP/TST (GPU) 1.1

:: DESCRIPTION

TSP/TST (GPU) (the top-scoring pair and top-scoring triplet) is the relative expression classification algorithms  for the graphics processing unit (GPU).

::DEVELOPER

the Price lab at ISB

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux/ WIndows/ MacOsX
  • Matlab

:: DOWNLOAD

  TSP/TST (GPU)

:: MORE INFORMATION

GeauxDock v2 – GPU Accelerated Molecular Docking

GeauxDock v2

:: DESCRIPTION

GeauxDock is an ultra-fast automated docking program, designed to predict how small ligands bind to pharmacologically relevant macromolecules. GeauxDock employs a novel hybrid force field and a Monte Carlo protocol for the efficient sampling of conformational space.

::DEVELOPER

The LONI Institute

:: SCREENSHOTS

n/a

:: REQUIREMENTS

  • Linux

:: DOWNLOAD

GeauxDock

:: MORE INFORMATION

Citation

GeauxDock: A novel approach for mixed-resolution ligand docking using a descriptor-based force field.
Ding Y, Fang Y, Feinstein WP, Ramanujam J, Koppelman DM, Moreno J, Brylinski M, Jarrell M.
J Comput Chem. 2015 Oct 15;36(27):2013-26. doi: 10.1002/jcc.24031. d

Chi8 v1 – GPU program for Detecting Significant Interacting SNPs with the Chi-square 8-df test

Chi8 v1

:: DESCRIPTION

Chi8 is a program that calculates the chi-square 8 degree of freedom test between all pairs of SNPs in a brute force manner on a Graphics Processing Unit.
Usman Roshan

::DEVELOPER

Usman Roshan

:: SCREENSHOTS

n/a

:: REQUIREMENTS

  • Linux

:: DOWNLOAD

 Chi8

:: MORE INFORMATION

Citation

Chi8: a GPU program for detecting significant interacting SNPs with the Chi-square 8-df test.
Al-Jouie A, Esfandiari M, Ramakrishnan S, Roshan U.
BMC Res Notes. 2015 Sep 14;8:436. doi: 10.1186/s13104-015-1392-5.

MaxSSmap v1 – GPU program for Mapping Divergent Short Reads to Genomes with the Maximum Scoring Subsequence

MaxSSmap v1

:: DESCRIPTION

MaxSSmap is a GPU program with the aim of achieving comparable accuracy to Smith-Waterman but with faster runtimes. MaxSSmap identifies a local region of the genome followed by exact alignment.

::DEVELOPER

Usman Roshan

:: SCREENSHOTS

n/a

:: REQUIREMENTS

  • Linux

:: DOWNLOAD

 MaxSSmap

:: MORE INFORMATION

Citation

BMC Genomics. 2014 Nov 15;15:969. doi: 10.1186/1471-2164-15-969.
MaxSSmap: a GPU program for mapping divergent short reads to genomes with the maximum scoring subsequence.
Turki T1, Roshan U.