An algorithm to assemble pathways from processes

To understand or to modify a biological pathway, the first step is to determine the patterns of coupling among its processes that are compatible with its input-output relation. Algorithms for this purpose have been devised for metabolic pathways, in which the reactions typically leave the enzymes unmodified. As shown here, one of these algorithms can also assemble molecular networks in which reactions modify proteins, if the proteins are included among the inputs to the reactions. Thus one procedure suffices to assemble pathways for metabolism, cytoplasmic signal transduction, and gene regulation.