It is possible to build a computer simulation of a linear biochemical pathway. This can be done by building a simple model that describes each intermediate through a differential equation. The differential equations can be written by invoking mass conservation. For example, for the linear pathway:
where  and  are fixed boundary species, the non-fixed intermediate  can be described using the differential equation:
The rate of change of the non-fixed intermediates  and  can be written in the same way:
To run a simulation the rates,  need to be defined. If mass-action kinetics are assumed for the reaction rates, then the differential equation can be written as:
If values are assigned to the rate constants, , and the fixed species  and the differential equations can be solved.