network-motif

Network Motif analysis using ESU algorithm (Java)

Test Drive

Prerequisites

• labelg program compiled for your computer. If you're working through the UWB Linux Lab, the provided executable will suffice. Otherwise you will need to compile and include your own: replace labelg with an identically named executable and change the mode to allow execution (chmod +x labelg). The source is available at http://cs.anu.edu.au/~bdm/nauty/ (to build, bash configure && make all).
• Mac/Linux platform, if you want to use the shell scripts. If you want to run this in Windows, you'll probably need to update the labelg program name (programName in Labeler.java).

Execution

Compile the code, then run the program on the master node:

$ ./compile.sh

$ ./run.sh datafile motif [--show-results]

# examples:

# motif size of 3, print canonical label counts:
$ ./run.sh data/Scere20131031CR.txt 3 --show-results

# motif size of 4, don't print results
$ ./run.sh data/test05 4

Data File Format

Text file, with each line containing a "from" node and a "to" node, as indicated by the string. These are interpreted to be undirected connections, so the ordering does not actually matter.

Example:

a b
b c
b d
d e

This represents the following graph:

 ___        ___        ___
| a | ---- | b | ---- | c |
 ---        ---        ---
             |
             |
            ___        ___
           | d | ---- | e |
            ---        ---