License¶

All code for ITM Probe (qmbpmn-tools) and CytoITMProbe written at the NCBI is released into Public Domain. The licenses of external components are indicated in the source packages.

References¶

Further details about ITM Probe can be found in the following references:

1. A. Stojmirovic and Y.-K. Yu. Information flow in interaction networks. J. Comput. Biol., 14 (8):1115-1143, 2007.

2. A. Stojmirovic and Y.-K. Yu. ITM Probe: analyzing information flow in protein networks. Bioinformatics, 25 (18):2447-2449, 2009.

Credits¶

• Aleksandar Stojmirovic and Yi-Kuo Yu designed the study, conducted the research and wrote the papers;

• Aleksandar Stojmirovic wrote the code for the qmbpmn-tools.

• Alexander Bliskovsky and Aleksandar Stojmirovic wrote together the code for CytoITMProbe.

Acknowledgments¶

ITM Probe (qmbpmn-tools package) is written in the Python programming language and relies on several open-source components:

• Numpy and Scipy libraries of scientific tools for Python;

• UMFPACK library for solving sparse systems of linear equations;

• Graphviz graph vizualization software;

• Sphinx Python documentation generator;

• Jinja2 template engine.

• Pyparsing

The web browser client code uses various Javascript routines from the NCBI. ECMAScrpit code and widgets for the SVG ‘Network Navigator’ were taken from Carto:Net.

All discrete network image color schemes were taken from the www.ColorBrewer.org site by Cynthia A. Brewer, Geography, Pennsylvania State University.

Protein interaction graphs for the web version were constructed using data from the BioGRID database.

CytoITMProbe uses Apache HttpComponents library for HTTP requests and Google gson for manipulating JSON files. The icons used in the graphical interface were taken from the Tango Icon Library, version 0.8.90.

We are grateful to Zvezdana Stojmirovic for help with the graphic design the ITM Probe web pages and interfaces.

News and Updates¶

• 30-Jan-2020. qmbpmn-tools 1.5.5 released - migration from python 2 to python 3.

• 01-Sep-2017. qmbpmn-tools 1.5.4 released - a bug fix and some other small changes.

• 03-Jul-2013. qmbpmn-tools 1.5.3 released - minor changes and bug fixes.

• 12-Mar-2012. CytoITMprobe 1.5 released.

• 02-Mar-2012. qmbpmn-tools 1.5.2 released - a bug fix for ITM Probe.

• 07-Feb-2012. qmbpmn-tools 1.5.1 released - minor changes and bug fixes for ITM Probe.

• 14-Dec-2011. qmbpmn-tools 1.5.0 released - minor changes mostly related to SaddleSum.

• 11-Jul-2011. ITM Probe 1.3.0 released, with updated web forms. It is now possible to retrieve an old job using its query ID.