Plant immunity is a highly dynamic process and requires dynamic modeling to capture the events of complexity mediated by the interaction between plant host and the attacking pathogen. The events of recognition are invoked by pathogen-based epitopes, while the subversion of host defenses are orchestrated by pathogen-originated effector molecules. The pathogen constitutes an immune signaling network inside the host cells. We model plant immune dynamics by using JIMENA-package, which is a java-based genetic regulatory network (GRN) simulation framework. It can efficiently compute network behavior and system states mediated by pathogenic perturbations. Here, we describe a step-by-step protocol to introduce the application of JIMENA-package to quantify immune dynamics in plant–pathogen interaction networks.