"metabolic models", what do we mean? There are a number of possible
meanings of such a term, and many of them are used in different
For our purposes a metabolic model is three things:
- the biomass reaction, which is a list of small compounds, co-factors, nucleotides, amino acids, and cell wall components needed to support growth. We think of this as the list of "required parts".
- a list of the compounds that can be transported into and out of the cell
- the reaction network that the cell uses to maintain its existence. This reaction network is encoded as a stoichiometric matrix.