Abstract: Disclosed is mapping complex inflammatory mechanisms in (Gulf War Illness) GWI to improve understanding of the immunologic underpinnings of GWI, the compounding effects of co-morbidity with post-traumatic stress disorder, and the potential of this co-morbidity to define a unique subtype of GWI. Predictive modeling assesses possible changes to putative treatments of GWI in the context of a probable PTSD diagnosis or lack thereof. A logic model is constructed to represent the neuroimmune system across the blood-brain barrier (BBB) connecting the central nervous system to blood-based system. Next, the model results of a GWI cohort are topologically compared with and without PTSD symptoms to mouse models of GWI in blood and use the corresponding neuroimmune states in a mouse brain to infer the blood-brain state of GWI subjects. This inference is then used to guide predictive modeling of treatment courses designed to return the overall neuroimmune system to healthy regulation.