1. A method of simulating a bio-transport system comprising: characterizing one or more elements to represent a bio-transport system of an organism or a portion thereof; constructing one or more mathematical representations that model one or more bio-transport dynamics for each element based on the characterization of said elements to form a configured simulation model; initializing said configured simulation model; executing said configured simulation model to obtain bio-transport dynamics data for one or more elements; and outputting information to a user based on at least a portion of said bio-transport dynamics data.