| ACS | Acetyl-CoA Synthase. |
| AGC | aspartate-glutamate carrier (see T4 in Appendix A) |
| AKG | α-ketoglutarate or 2-oxoglutarate |
| ANT | ADP/ATP exchanger. |
| ARGASE | arginase |
| ASS1_ASL_FH | argininosuccinate synthase + argininosuccinate lyase + fumarate hydratase |
| ASYNT | ATP Synthase. |
| ASPUP | Uptake of aspartate. |
| ATPASE | ATP usage. |
| BM | 0.18 SERc + 0.11 Palmitate_c + 0.04 XTPc + 0.19 GLNc + 0.17 GLUTc + 0.7 ASPc + 0.05 ARGc + 0.12 PYRc + 4 ATPc => 1 Biomass + 4 ADPc + 4 Pic. |
| CL (ACL) | (ATP) Citrate Lyase. |
| CPS1_OTC | carbamoyl phosphate synthase 1 + Ornithine transcarbamylase |
| CS | Citrate Synthase. |
| DPH | pH difference between inside and outside mitochondria. |
| DPSI | mitochondrial membrane potential. |
| ENOMUT | Enolase + Phosphoglycerate Mutase. |
| ETC | Electron Transport Chain or Respiratory Chain |
| FBA | Flux Balance Analysis. |
| FVA | Flux Variability Analysis. |
| G1 | hexokinase + phosphoglucose isomerase. |
| G2 | phosphofructokinase + aldolase + triose-phosphate isomerase. |
| G3 | Glyceraldehyde-3P Dehydrogenase + phosphoglycerate kinase. |
| GG3 | triose phosphate isomerase + aldolase + fructose -1,6-biphosphatase. |
| GG4 | phosphogluco isomerase + glucose-6-phosphatase. |
| GLS1 | Glutaminase. |
| GLNUP | Uptake of Glutamine. |
| GLUCUP | Uptake of glucose. |
| GLUD1 | Glutamate Dehydrogenase. |
| GOT | Glutamate Oxaloacetate Transaminase. |
| IDH | Aconitase + Isocitrate dehydrogenase. |
| L | Proton leak of the mitochondrial membrane. |
| LACIO | Input/Output of lactate. |
| LDH | Lactate Dehydrogenase. |
| MAS | Malate/Aspartate Shuttle. |
| ME | Malic Enzyme. |
| MDH | Malate Dehydrogenase |
| NAGS_ACY | N-acetylglutamate synthase + Amino Acylase (ornithine synthesis from glutamate). |
| NIG | for nigericine, exchange of DPH and DPSI. |
| NOS | NO synthase. |
| NUC | Nucleotide (XTP) Synthesis. |
| OGC | Oxoglutarate carrier (see T2 in Appendix A). |
| ORNT1 | Ornithine/Citrulline + H+ exchanger. |
| ORNT2 | Ornithine/H+ exchanger. |
| PDH | Pyruvate Dehydrogenase. |
| PEPCK | PhosphoEnolPyruvate Carboxy Kinase. |
| PK | Pyruvate Kinase. |
| PL1 | Synthesis of PhosphoLipids. |
| PP1 | Oxidative part of PPP. |
| PP2 | non-oxidative part of PPP. |
| PPP | Pentose Phosphate Pathway. |
| PYC | Pyruvate Carboxylase. |
| RC1 | Complex I of Respiratory Chain. |
| RC2 | succinate dehydrogenase + fumarase. |
| RC34 | Complex III+IV of Respiratory Chain. |
| SEROUT | Output of serine. |
| SERSYNT | Serine Synthesis = Dehydrogenase + Transaminase and Phosphatase. |
| SLP (Substrate Level Phosphorylation) | 2-oxoglutarate dehydrogenase + succinate thiokinase |
| XTP | Nucleotides |