Minimal version of the physical network model inference prototype.

Inputs: protein-DNA and protein-protein interaction data, knockout gene 
expression data.

Outputs: network annotations written in formats for cytoscape visualization.

commands:

./generate_subnetworks1 genes.txt genes.txt locdata_feb_2003.txt 0.001 yeast_pp_5_03.cgi rosetta_genes.txt rosetta_exps.txt 0.02 rosettapvalues.txt logratio.txt subnetworks.sif subnetworksdir.txt subnetworkssign.txt subnetworksko.txt subnetworkskopairs.txt

The meaning for each argument is in generate_subnetworks1.c.

