In the folder you will have the following:

1. bnra.m - BNRA MATLAB script
2. sample - folder containing some signaling pathways from KEGG in XML format 

1. Open Matlab on Windows.

2. From The GUI click "Open" which will open the file explorer.

3. Find the file BNRA (if should be on the same folder as WinPython) and click "Open" and "Run". A file entry box will appear.

4. For field "Enter the file name of the network to be analyzed" (in fasta format) give the KEGG ID of the path to be analyzed, then click OK.

5. The current state of the network is visually displayed.

6. For field "Please select the protein you want to perturb" select one among the proteins from the list of proteins which you want to perturb, then click OK.

7. For field "Please select the type of interaction using which the selected node is perturbed with a new node" select the type of interaction, then click OK.

8. For field "Enter the new incoming node" give a random number to the new node being introduced to perturb the network, then click OK.

9. Wait for the results. The new state of the network is displayed.