Methods for identifying disease-related pathways that can used to identify drug discovery targets, to identify new uses for known drugs, to identify markers for drug response, and related purposes. The system uses a second antenna having a dual port feed and a reflector, the second antenna having a second aperture of a second size, which is two or more times the first size, and being operative to form a plane wave. The user andor software contacts an authorized representative of the software to obtain authorization information which may be downloaded directly to the software or provided to the user for entry. Second, the memory element dependency graph of each peripheral partition of the scanned circuit has a tree structure.