What is a model?

When we say that we now support generation, maintenance, and use of
"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
contexts.

For our purposes a metabolic model is three things:

1. 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".
2. a list of the compounds that can be transported into and out of the cell
3. the reaction network that the cell uses to maintain its existence.  This reaction network is encoded as a stoichiometric matrix.
   

We have defined a precise encoding of models, so we can import and export them, as well as updating them to reflect constantly improving estimates of the roles of specific genes and knowledge of phenotype.