Figure 4.

Specification of model sub-parts. (A) Original full model, from which a few pathways are selected. (B) Further selections of reactions from the subset of pathways. Deleted molecules, reactions, and enzymes are indicated by boxes with blue crosses. In some cases, deleting molecules leads to dangling reactions (red dashed boundary), which lack one or more reactants. The system identifies these. In addition to removal of extraneous reactions and reactants, the experiment specification may involve alteration of parameters, such as the concentration of a molecule that is buffered in the experiment. This is illustrated as orange boxes around the molecule TOR_clx. Finally, the model specification also defines the mapping between the experimental names for stimulus or readout molecules, to the corresponding names for these molecules as used in the model.