What is a metabolic 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 consists of three components:

1. The network of biochemical reactions and transmembrane transporters the cell uses to produce the machinery it requires to grow divide and survive. This reaction network is encoded as a stoichiometric matrix.
2. A list of rules called gene-protein-reaction associations that describe how gene activity is linked to reaction activity. For example, gene A and gene B form a protein complex that catalyzes reaction 1.
   
3. A biomass reaction, which is a list of small molecules, co-factors, nucleotides, amino acids, lipids, and cell wall components needed to support growth and division.  We think of this as the list of "required parts".

In this tutorial, we describe how these models are generated in the SEED and how they are used to generate predictions of cell behavior. We will also describe the process by which models must be curated to improve the accuracy of predictions.