The code and examples listed in the core directory are the essential materials to use and reproduce the method that is presented in the paper "A Molecular Communication model for cellular metabolism".
The content of the auxillary directory are extra file versions and exploratory assessments that are in various degrees of deprecation.
The FBA simulations for B. theta and M. smithii are available in the https://narrative.kbase.us/narrative/14662 and https://narrative.kbase.us/narrative/14663 KBase Narratives, respectively.