I discuss a systematic approach to the modeling of biological, biochemical and related systems which starts from individual-based models, and then goes on to derive from these the corresponding deterministic equations which are valid when the size of the system is large. The formalism also applies to spatially explicit models, and I will compare the governing deterministic equations for these systems to those which are normally written down on phenomenological grounds. The case of the diffusion of two types of particle, where extra nonlinear terms reflect the depletion of resources on which the particles rely, will be examined in detail.