Modeling an entire system is almost always harder than modeling individual pieces of a system. As such, I expect that you almost always start with individual p

Modeling an entire system is almost always harder than modeling individual pieces of a system. As such, I expect that you almost always start with individual parts modeled, and then you are trying to combine multiple models together. Stated differently, no model can really account for interactions that are invisible to it. As such, unless you are aiming at a giant model that encompasses everything, it seems unlikely that you will be able to use some modeling tools that are made to do this sort of stuff directly.