PWComp is a standalone Java based application that uses BioCyc as its primary source of data. Data parsers take the information contained in the BioCyc database and places it in a datastore container class which is a "super repository" for specific class representations of reactions, compounds pathways, etc.

The computational engine operates on these class structures, converting the Pathway Graph representation into an enzyme graph and then extracting E.C numbers in order to generate a similarity matrix and perform the Heyman Algorithm to compute an overall similarity score for a given pair of pathways.

The user interacts with these classes through the GUI which retreives the Pathway Graphs from the datastore.