Figure 2

Simplified view for the stoichiometric model of ruminant mammary metabolism with no long-chain fatty acid oxidation. The complete model is detailed in a SBML Additional file 1. Eleven nodes are considered as pivots (green nodes), that is, intermediary metabolites which are not accumulated in the cell. The model is built by adding 26 specific reactions to the ruminant mammary to the generic model of [23]. A treatment is characterized by a set of input nodes (yellow nodes), quantitatively described in mmol/h/half udder. Nutrients contained in the milk are considered as output nodes. The node “Fatty acid synthesis” is an abstraction for 14 reactions corresponding to C(4:0), C(6:0), …C(16:0) from primerC2 and primerC4. Note that, depending on the treatment, the role of nonessential amino acids may change from input to output according to the balance of the amino-acid considered. The node “peptide” summarizes the ATP cost of protein synthesis and protein degradation. Notably, the stoichiometry of reactions was adjusted in order to balance carbon exchanges, including CO2. This is a key point in order to compute exact allocation tables in the following stages. Additional literature-based information allows us to generate additional linear constraints on some reactions fluxes.