Computational Bioinformatics and Bioimaging Laboratory


 
        (caBIG PUGSVM)

caBIG PUGSVM - Introduction

PUGSVM (Phenotypic Up-regulated Gene Support Vector Machine) is a caBIGTM (cancer Biomedical Informatics Grid) analytical tool for multiclass gene selection and classification. PUGSVM addresses the problem of imbalanced class separability, small sample size and high gene space dimensionality, where multiclass gene markers are defined by the union of one-versus-everyone phenotypic up-regulated genes, and used by a well-matched one-versus-rest support vector machine. PUGSVM provides a simple yet more accurate strategy to identify statistically-reproducible mechanistic marker genes for characterization of heterogeneous diseases.

 
caBIG PUGSVM - Download Files

 

caBIG PUGSVM - Installation Guide

  • Install Java Application for Windows

    1. Download two files 'MCRInstaller.part1.rar' and 'MCRInstaller.part2.rar' on the download page and uncompress them, which will generate an unzipped file 'MCRInstaller.exe'.
    2. Run 'MCRInstaller.exe'.
    3. Download the file 'PUGSVM_Java_WINDOWS_v1.0.zip' on the download page and uncompress it. All necessary files for the caBig PUGSVM tool are contained  in the unzipped folder 'PUGSVM_Java_WINDOWS_v1.0'.
    4. For detailed instruction on how to use the tool, please refer to the readme file in the folder 'PUGSVM_Java_WINDOWS_v1.0'.
  • Install Java Application for Linux

    1. Download three files 'MCRInstaller_Linux.part1.rar', 'MCRInstaller_Linux.part2.rar' and 'MCRInstaller_Linux.part3.rar' on the download page and uncompress them, which will generate an unzipped file 'MCRInstaller.bin'.
    2. Run 'MCRInstaller.bin'.
    3. Download the file 'PUGSVM_Java_LINUX_v1.0.zip' on the download page and uncompress it. All necessary files for the caBig PUGSVM tool are contained  in the unzipped folder 'PUGSVM_Java_LINUX_v1.0'.
    4. For detailed instruction on how to use the tool, please refer to the readme file in the folder 'PUGSVM_Java_LINUX_v1.0'.
  • Install Matlab Toolbox

    1. Download the file 'PUGSVM_MatlabPackage_v1.0.zip' on the download page and uncompress it. All necessary files for the caBig PUGSVM tool are contained  in the unzipped folder 'PUGSVM_MatlabPackage_v1.0'.
    2. For detailed instruction on how to use the tool, please refer to the readme file in the folder 'PUGSVM_MatlabPackage_v1.0'.
 

 

 

 

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Copyright 2004, Computational Bioinformatics and Bioimaging Laboratory (CBIL), Advanced Research Institute, Virginia Tech.

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