Outside of laboratories, microbial communities (biofilms and other types) often exist in relatively stable environments where, on average, resource quality and quantity are predictable. In these conditions, these communities are able to organize into tuned chemical factories, efficiently turning resources into biomass and waste byproducts. To do so, physical, chemical, and biological constraints must be accomodated. In this seminar, techniques to model this organization will be discussed. In particular, the importance of coupling microscale metabolic information to community scale transport processes will be emphasized.