First edit the sim.cfg file.

Next run gsim:

>./gsim

this will generate files:

dependencies
filelist
Afiles
sim.gen
Bfiles

Next run dsim:

>./dsim

This will generate files

simf_A001
simf_A002
simf_A003
simf_A004
...
simf_B001
simf_B002
simf_B003
simf_B004
...

These files map gene identifiers (which are the integers 0, 1, 2, ...) to intensities, one "array" per file.

To view the distributions run gene_expression_plotter.pl, which takes two arguments, the list of files for group1 and the list of files for group 2. These are generated automatically when you run dsim and are saved to Afiles and Bfiles. The distributinos are written to standard out. For each gene three distributions are written, the first combines both groups, the second gives group 1 and the thrid gives group 2.

> perl gene_expression_simulator.pl Afiles Bfiles > distributions.txt