This technology relates to a mathematical model of a biological process having a complex spatial geometry. The methods of this invention can be employed to model many biological processes, such as cell signaling in general and vision in particular. These models can also be used to model the pathology underlying diseases characterized by disrupted signaling pathways, and to identify target proteins at an appropriate site in a signal transduction network such that modulation of the target proteins elicits therapeutic effects. Methods of modeling diffusion processes, as well as machine-readable products embodying the methods are also disclosed. Issued US Patent 7113898.