Figure 1

Using “isa” reactions. Yeast 5 uses “isa” reactions to encapsulate specific chemical species within more general classes. For example, A) the specific species inositol-P-ceramide-A “isa” inositol phosphoceramide (IPC). In turn, IPC “isa” complex sphingolipid. B) Complex sphingolipids participate in the stoichiometrically constrained reaction which produces the species “lipid”. C) The lipid species is a component of biomass. This hierarchical model structure embeds logic in the biomass definition: biomass consists of L-alanine AND phosphatidylcholine AND (inositol-P-ceramide-A OR Inositol-P-ceramide-B OR any of the 88 other complex sphingolipids included in the reconstruction). A model user is free to constrain the fluxes which produce specific complex sphingolipids to model an observed lipid composition, or may leave the model unconstrained if the more general biomass definition is sufficient for their needs