Table 1 Kinetics examples for ten defined kinetics types (K type)
From: SBMLKinetics: a tool for annotation-independent classification of reaction kinetics for SBML models
K type | BIOMD | Reaction | Kinetic law |
|---|---|---|---|
ZERO | 5 | EmptySet \(\rightarrow\) Y | Cell\(\cdot\)k1aa |
UNDR | 5 | CP \(\rightarrow\) C2 | Cell\(\cdot\)CP\(\cdot\)k9 |
UNMO | 12 | \(\rightarrow\) PX | k_tl\(\cdot\)X |
BIDR | 1 | B \(\rightarrow\) BL | Comp1\(\cdot\)(kf_0\(\cdot\)B - kr_0\(\cdot\)BL) |
BIMO | 88 | s172 \(\rightarrow\) s135 | c1\(\cdot\)g\(\cdot\)s173\(\cdot\)(s172–s135) |
MM | 4 | MI \(\rightarrow\) M | Cell\(\cdot\)MI\(\cdot\)V1\(\cdot\)pow(K1 + MI, − 1) |
MMCAT | 10 | MKK \(\rightarrow\) MKK_P | uVol\(\cdot\)k3\(\cdot\)MKKK_P\(\cdot\)MKK/(KK3 + MKK) |
HILL | 55 | \(\rightarrow\) cLm | Compartment\(\cdot\)(n1\(\cdot\)pow(cXn, a)/ (pow(g1, a) + pow(cXn, a))) |
FR | 3 | \(\rightarrow\) M | Cell\(\cdot\)(1 + − 1\(\cdot\)M)\(\cdot\) V1\(\cdot\)pow(K1 + − 1\(\cdot\)M + 1, − 1) |
NA | 160 | \(\rightarrow\) timm | WholeCell\(\cdot\)((1 - pow(1 - prct, npt))\(\cdot\)tccctimp + pow(1 - prct, npt)\(\cdot\)tcdvpmt)\(\cdot\)timp |