Tools

Students use several software tools in this course. This page presents tutorials, background information and example data for these tools.

MATLAB®

MATLAB® Tutorial (Courtesy of Gergana Bounova. Used with permission.)

  • Slides (PDF)
  • Routines (ZIP) (The ZIP file contains: 19 .m files, and 1 .mat file.)
  • Class Datasets (ZIP) (The ZIP file contains: 2 .wk1 files and 1 .txt file.)

Kleinberg Prestige Routine (M) (Courtesy of Mo-Han Hsieh. Used with permission.)

Sergei Maslov's "Rewiring" Routines (ZIP) (The ZIP file contains: 3 .m files and 1 .txt file.) (Courtesy of Sergei Maslov.)
These relate to the paper Maslov, S., and K. Sneppen. "Specificity and Stability in Topology of Protein Networks." Science 296 (May 3, 2002): 910-913.

Pearson Degree Correlation (ZIP) (The ZIP file contains: 2 .m files.)

Note: always test a routine on a simple example for which you know already what the answer should be.

Mfinder

Mfinder is a network motifs detection tool. Software, source code, a manual and supporting materials are available from Uri Alon's homepage, select the "Network Motif Software" link.

Pajek

Pajek (Program for Large Network Analysis) is a free software package.

UCINET

UCINET is a software package for the analysis of social network data as well as other 1-mode and 2-mode data.