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Python Package - qmbpmn-tools

qmbpmn-tools is a collection of Python libraries and scripts for network analysis developed by the QMBP group at the NCBI. It consists of the ITM Probe library and executable script, the routines for managing ITM Probe and SaddleSum web sites, a package manager and miscellaneous libraries and utilities.

Warning

qmbpmn-tools is in heavy development and may change in many ways. We do not support this package but only release it as a reference implementation. This documentation is therefore incomplete and should be considered as short installation notes rather than as user’s manual. The best way to obtain detailed information is to actually read the source code.

Prerequisites

qmbpmn-tools requires a number of standalone programs and Python packages. All are open source and can be downloaded and installed on UNIX, Windows and Mac OSX machines. Please consult the documentation of individual packages for information of how to install them. The prerequisites are:

  • Python 3.7 complied with SQLite support.

  • SaddleSum standalone program for SaddleSum website functionality.

  • Graphviz graph visualization software. Not necessary for CytoITMprobe.

  • Numpy and Scipy libraries of scientific tools for Python. Numpy should be version 1.3 or higher, while Scipy should be version 0.7 or higher.

  • Pyparsing

  • SciKits.umfpack Python package (Optional but highly recommended). It requires UMFPACK library for solving sparse systems of linear equations. Ensure that UMFPACK is compiled with good BLAS, otherwise ITM Probe performance will greatly suffer.

  • Jinja2 template engine. Not necessary for CytoITMprobe.

  • Sphinx Python documentation generator (version 1 or higher). Sphinx additionally requires docutils and Pygments packages. Not necessary for CytoITMprobe.

Downloading and Installing

The source code is available on the NCBI FTP site (ftp://ftp.ncbi.nih.gov/pub/qmbpmn/qmbpmn-tools/) as a tar.gz archive. Extract the archive to a temporary directory, and install it in the standard way:

python setup.py install

The setup program will install the package and also place several executable scripts in your path.

Components

qmbpmn-tools source package consists of four subdirectories:

  • scripts/ contains executable programs (i.e. Python scripts) such as

    • itmprobe - standalone ITM Probe,

    • qmbpmn-deploy - a script to deploy the website,

    • qmbpmn-server - a rudimentary deployment server,

    • qmbpmn-datasets - package manager,

    • cluster - a script to cluster vectors using the method described in Hamaneh MB, Yu YK. PLoS One. 2014 Oct 31;9(10):e110936

Most scripts have some help available. Use:

<script-name> -h

to print help to the screen.

  • ITMProbe/ contains ITM Probe core library

  • web/ contains Python and resource files for the ITM Probe, SaddleSum and DeCoaD web sites.

  • common/ contains shared subpackages as well as code obtained from other open-source projects.

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Maintained by Mehdi Bagheri Hamaneh. Last update: Dec 22, 2023.