Table 3.
Network characteristics and FBA simulations in Arabidopsis GSMs.
| Items model | Cell type | Model format | Cell maintenance | Objective function | BOF included |
|---|---|---|---|---|---|
| Poolman | Heterotrophic | ScrumPy and SBML | NGAM | Minimize total flux | PoolmanBOF |
| AraGEM | Photosynthetic and Heterotrophic | SBML | GAM | Minimize photon/sucrose uptake of growth rate | AraGEMBOF |
| Radrich | Unknown | SBML | Not included | Not included | Not included |
| iRS1597 | Photosynthetic and Heterotrophic | Excel | GAM | Maximize biomass | AraGEMBOF |
| Mintz-Oron | Photosynthetic and Heterotrophic | SBML | GAM | Minimize metabolic adjustment (MOMA) | AraGEMBOF |
| iAT1475 | Photosynthetic and Heterotrophic | Excel | GAM | Maximize IPP production | AraGEMBOF |
| Cheung | Photosynthetic and Heterotrophic | ScrumPy and SBML | GAM and NGAM | Five objective functions[a] | Biomass as constraints |
| AraCore | Photosynthetic and Heterotrophic | SBML | Not included | Maximize biomass and energy efficiency | AraCoreBOF |
“PoolmanBOF” indicates the biomass objective function included in the Poolman model; “AraGEMBOF” indicates the biomass objective function included in the AraGEM model; “AraCoreBOF” indicates the biomass objective function included in the AraCore model. GAM, growth associated maintenance; NGAM, non-growth associated maintenance. [a]5 objective functions are minimization of overall flux, maximization of biomass, minimization of glucose consumption, maximization of ATP production and maximization of NADPH production.