Pathway Logic (PL) is a general system for modeling signal transduction and other cellular processes with the objective of understanding how cells work. Models are derived from knowledges bases of experimental findings (datums) and rules formalizing local process steps such as post translational modification, translocation, or transcription/translation. The Pathway Logic Assistant (PLA) is a collection of visualization and reasoning tools that allow users to derive specific executable models by specifying of an initial state. The resulting network of rule instances describes possible behaviors of the modelled system. Subnets and pathways can then be computed (they are not hard wired) by specifying states to reach and/or to avoid. The talk will begin with a brief introduction to PL and the PLA. We will then describe some recent applications, including explaining drug effects; modeling host virus interactions; and experience importing models from the Macrophage Map.