Ecosim provides a dynamic simulation capability at the ecosystem level, with key initial parameters inherited from the base Ecopath model. See Ecosim Inputs? and Ecosim Outputs? for links to instructions for using Ecosim.
The key computational aspects are in summary form:
Ecosim uses a system of differential equations that express biomass flux rates among pools as a function of time varying biomass and harvest rates, (for equations see Walters et al., 1997; Walters et al., 2000; Christensen and Walters, 2004). Predator prey interactions are moderated by prey behaviour to limit exposure to predation, such that biomass flux patterns can show either bottom-up or top down (trophic cascade) control (Walters et al., 2000. By doing repeated simulations Ecosim allows for the fitting of predicted biomasses to time series data.