Table 3.
List of the abbreviations used to define the constraints during the optimisation step.
| Abbreviation | Definition |
|---|---|
| R | All reactions present in the model |
| RK | The set of reactions with known ranges, such as: tissue exchangers, urine secretion reactions |
| B | The set of metabolites with known basal concentration levels or ranges in the blood |
| RB | The set of blood storage reactions associated with the metabolites in B |
| MAA | The set of metabolites in the muscle amino acid storage |
| RMAA | The set of muscle amino acids storage reactions associated with metabolites in MAA |
| RCS | The set of added transport reactions from the cytoplasm to the extracellular space (e.g. met[c] ↔ met[e]) The protein sources which are stored and degraded |
| P | The set of protein sources which are stored and degraded |
| RPD | The set of protein degradation reactions |
| RPS | The set of protein storage reactions |
| RNU | The set of nutrient uptake reactions (→ glc[bl]) |
| C | The set of carbon sources which are stored and degraded |
| RC | The set of reactions associated with storages in C |