From 2007.igem.org

We realized a reaction network as a system of ODEs. Clearly we need to guess working hypothesis:

• Component concentrations don't vary with respect to space

Whether it is a good assumption depends on time and space scales. In a yeast cell molecular diffution is sufficiently fast to mix proteins in less than one minute

• Component concentrations are continuous functions of time

This is true if the number of molecules of each species in the reaction volume is sufficiently large

Other important assumptions are the following:

• Transcription factor timescales are much larger than protein-protein interactions timescales
• Input changes are very rapid

We will use this assumptions to simplify our modeling

ODEs are very useful to represent molecular interaction. Indeed, applying a simple set of rules we can represent arbitrarily complex reaction networks as a set of coupled ODEs!