Table 1.
List of biomass formulations that were benchmarked in the present study
| GEM | Biomass abbreviation | References | Summary of the biomass reaction |
|---|---|---|---|
| Recon family (1, 2, and 3) | R_generic | (Brunk et al., 2018; Duarte et al., 2007; Thiele et al., 2013) | dNTPs + NTPs + amino acids + lipid precursors + carbohydrates ➞ H+ + ADP + Biomass |
| HMR 2.0 (biomass components) | HMR_gen | (Mardinoglu et al., 2014) | dNTPs + NTPs + amino acids + lipid precursors + cofactors and vitamins + glycogen ➞ H+ + ADP + Biomass |
| Human 1 | Human1_gen | (Robinson et al., 2020) | dNTPs + NTPs + amino acids + lipid precursors + glycogen storage pool + metabolite pool + protein pool + cofactor pool ➞ H+ + ADP + Biomass |
| iHsa | iHsa_gen | (Blais et al., 2017) | dNTPs + NTPs + amino acids + proteins + bile acid + glycogen storage pool + lipid precursors + misc metabolites ➞ H+ + ADP + Biomass |
| Recon 3 (maintenance biomass)a | R3_main | (Brunk et al., 2018) | NTPs + amino acids + lipid precursor s + carbohydrates ➞ H+ + ADP + Biomass |
| Recon 3 (noTrTr biomass)b | R3_noTrTr | (Brunk et al., 2018) | NTPs + lipid precursors + carbohydrates ➞ H+ + ADP + Biomass |
| HMR 2.0 (cancer renal biomass) | HMR_renal | (Mardinoglu et al., 2014) | dNTPs + NTPs + amino acids + lipid precursors + carbohydrates + vitamin pool + glycerides + cholesterol esters ➞ H+ + ADP + Biomass |
| BOFdat | BOFdat_Biomass | (Lachance et al., 2019) | dNTPs + NTPs + amino acids + lipid precursors + coenzymes and inorganic ions + specific metabolites ➞ H+ + ADP + Biomass |
a
Recon 3 maintenance biomass represents the Recon generic biomass reaction without replication precursors.
b
Recon 3 noTrTr biomass reaction represents the Recon generic biomass reaction without replication, transcription, and translation.