Metabolic Component Library for CellML

Matthias Koenig [1] & Randall Britten [2]
[1] Charite Berlin, matthias.koenig@charite.de
[2] Auckland Bioengineering Institute

Implementation of standardized reaction kinetics in CellML for reuse in metabolic models. The library covers the metabolic function definitions for processes from COPASI 4.8 (Bulid 35).

Components

Substrate(s) : S (S1, S2, ...)
Product(s) : P (P1, P2, ... )
Inhibitor(s) : I (I1, I2, ...)
Activator(s) : A (A1, A2, ...)
Modifier(s) : M (M1, M2, ...)

AllostericInhibitionEmpirical

(Validation Errors: 0) J [mM_per_second] S [mM] P [mM] I [mM] V_f [mM_per_second] V_b [mM_per_second] Km_S [mM] Km_P [mM] n [dimensionless] Ki [mM]
Mechanisms UniUniRev_I

AllostericInhibitionMWC

(Validation Errors: 1) J [mM_per_second] S [mM] I [mM] V [mM_per_second] Km_S [mM] n [dimensionless] L [dimensionless] Ki [mM]
Mechanisms UniUniIrrev_I UniBiIrrev_I UniNullIrrev_I

BiIrrev

(Validation Errors: 0) J [mM_per_second] S1 [mM] S2 [mM] V [mM_per_second] Km_S1 [mM] Km_S2 [mM]
Mechanisms BiNullIrrev BiBiIrrev BiUniIrrev

CatalyticActivationIrrev

(Validation Errors: 0) J [mM_per_second] S [mM] A [mM] V [mM_per_second] Km_S [mM] Km_A [mM]
Mechanisms UniUniIrrev_A UniBiIrrev_A UniNullIrrev_A

CatalyticActivationRev

(Validation Errors: 0) J [mM_per_second] S [mM] P [mM] A [mM] V_f [mM_per_second] V_b [mM_per_second] Km_S [mM] Km_P [mM] Km_A [mM]
Mechanisms UniUniRev_A

CompetitiveInhibitionIrrev

(Validation Errors: 0) J [mM_per_second] S [mM] I [mM] V [mM_per_second] Km_S [mM] Ki [mM]
Mechanisms UniUniIrrev_I UniBiIrrev_I UniNullIrrev_I

CompetitiveInhibitionRev

(Validation Errors: 0) J [mM_per_second] S [mM] P [mM] V_f [mM_per_second] V_b [mM_per_second] I [mM] Km_S [mM] Km_P [mM] Ki [mM]
Mechanisms UniUniRev_I

ConstantFluxIrrev

(Validation Errors: 0) J [mM_per_second] V [mM_per_second]
Mechanisms UniNullIrrev UniUniIrrev UniBiIrrev BiBiIrrev BiUniIrrev

Hill1ModifierRev

(Validation Errors: 0) J [mM_per_second] S [mM] P [mM] M [mM] V [mM_per_second] Keq [dimensionless] Km_S [mM] Km_P [mM] Km_M [mM] a [dimensionless] h [dimensionless]
Mechanisms UniUniRev_M

Hill2ModifierRev

(Validation Errors: 0) J [mM_per_second] S [mM] P [mM] M1 [mM] M2 [mM] V [mM_per_second] Keq [dimensionless] Km_S [mM] Km_P [mM] Km_M1 [mM] Km_M2 [mM] a_A [dimensionless] a_B [dimensionless] a_AB [dimensionless] h [dimensionless]
Mechanisms UniUniRev_M2

HillIrrev

(Validation Errors: 1) J [mM_per_second] S [mM] V [mM_per_second] Km_S [mM] n [dimensionless]
Mechanisms UniNullIrrev UniUniIrrev UniBiIrrev

HillRev

(Validation Errors: 0) J [mM_per_second] S [mM] P [mM] V [mM_per_second] Keq [dimensionless] Km_S [mM] Km_P [mM] h [dimensionless]
Mechanisms UniUniRev

HyperbolicModifierIrrev

(Validation Errors: 0) J [mM_per_second] S [mM] M [mM] V [mM_per_second] Kd [mM] Km_S [mM] a [dimensionless] b [dimensionless]
Mechanisms UniNullIrrev_M UniUniIrrev_M UniBiIrrev_M

HyperbolicModifierRev

(Validation Errors: 0) J [mM_per_second] S [mM] P [mM] M [mM] V_f [mM_per_second] V_b [mM_per_second] Kd [mM] Km_S [mM] Km_P [mM] a [dimensionless] b [dimensionless]
Mechanisms UniUniRev_M

IsoUniUni

(Validation Errors: 0) J [mM_per_second] S [mM] P [mM] V [mM_per_second] Keq [dimensionless] Ki [mM] Km_S [mM] Km_P [mM]
Mechanisms UniUniRev

MassActionBiBiRev

(Validation Errors: 0) J [mM_per_second] S1 [mM] S2 [mM] P1 [mM] P2 [mM] k_f [per_mM_per_second] k_b [per_mM_per_second]
Mechanisms BiBiRev

MassActionBiIrrev

(Validation Errors: 0) J [mM_per_second] S1 [mM] S2 [mM] k_f [per_mM_per_second]
Mechanisms BiNullIrrev BiBiIrrev BiUniIrrev

MassActionBiUniRev

(Validation Errors: 0) J [mM_per_second] S1 [mM] S2 [mM] P [mM] k_f [per_mM_per_second] k_b [per_second]
Mechanisms BiUniRev

MassActionUniBiRev

(Validation Errors: 0) J [mM_per_second] S [mM] P1 [mM] P2 [mM] k_f [per_second] k_b [per_mM_per_second]
Mechanisms UniBiRev

MassActionUniIrrev

(Validation Errors: 0) J [mM_per_second] S [mM] k_f [per_second]
Mechanisms UniNullIrrev UniUniIrrev UniBiIrrev

MassActionUniUniRev

(Validation Errors: 0) J [mM_per_second] S [mM] P [mM] k_f [per_second] k_b [per_second]
Mechanisms UniUniRev

MichaelisMentenIrrev

(Validation Errors: 0) J [mM_per_second] S [mM] V [mM_per_second] Km_S [mM]
Mechanisms UniNullIrrev UniUniIrrev UniBiIrrev

MichaelisMentenRev

(Validation Errors: 0) J [mM_per_second] S [mM] P [mM] V_f [mM_per_second] V_b [mM_per_second] Km_S [mM] Km_P [mM]
Mechanisms UniUniRev

MixedActivationIrrev

(Validation Errors: 0) J [mM_per_second] S [mM] A [mM] V [mM_per_second] Kac [mM] Kas [mM] Km_S [mM]
Mechanisms UniUniIrrev_A UniBiIrrev_A UniNullIrrev_A

MixedActivationRev

(Validation Errors: 0) J [mM_per_second] S [mM] P [mM] A [mM] V_f [mM_per_second] V_b [mM_per_second] Kac [mM] Kas [mM] Km_S [mM] Km_P [mM]
Mechanisms UniUniRev_A

MixedInhibitionIrrev

(Validation Errors: 0) J [mM_per_second] S [mM] I [mM] V [mM_per_second] Kis [mM] Kic [mM] Km_S [mM]
Mechanisms UniUniIrrev_I UniBiIrrev_I UniNullIrrev_I

MixedInhibitionRev

(Validation Errors: 0) J [mM_per_second] S [mM] P [mM] I [mM] V_f [mM_per_second] V_b [mM_per_second] Kis [mM] Kic [mM] Km_S [mM] Km_P [mM]
Mechanisms UniUniRev_I

NoncompetitiveInhibitionIrrev

(Validation Errors: 0) J [mM_per_second] S [mM] V [mM_per_second] Km_S [mM] I [mM] Ki [mM]
Mechanisms UniUniIrrev_I UniBiIrrev_I UniNullIrrev_I

NoncompetitiveInhibitionRev

(Validation Errors: 0) J [mM_per_second] S [mM] P [mM] V_f [mM_per_second] V_b [mM_per_second] Km_S [mM] Km_P [mM] I [mM] Ki [mM]
Mechanisms UniUniRev_I

OrderedBiBi

(Validation Errors: 0) J [mM_per_second] S1 [mM] S2 [mM] P1 [mM] P2 [mM] V_f [mM_per_second] V_b [mM_per_second] Keq [dimensionless] Km_S1 [mM] Km_S2 [mM] Km_P1 [mM] Km_P2 [mM] Ki_S1 [mM] Ki_S2 [mM] Ki_P1 [mM]
Mechanisms BiBiRev

OrderedBiUni

(Validation Errors: 0) J [mM_per_second] S1 [mM] S2 [mM] P [mM] V_f [mM_per_second] V_b [mM_per_second] Keq [per_mM] Km_S1 [mM] Km_S2 [mM] Km_P [mM] Ki_S1 [mM]
Mechanisms BiUniRev

OrderedUniBi

(Validation Errors: 0) J [mM_per_second] S [mM] P1 [mM] P2 [mM] V_f [mM_per_second] V_b [mM_per_second] Keq [mM] Km_S [mM] Km_P1 [mM] Km_P2 [mM] Ki_P1 [mM]
Mechanisms UniBiRev

PingPongBiBi

(Validation Errors: 0) J [mM_per_second] S1 [mM] S2 [mM] P1 [mM] P2 [mM] V_f [mM_per_second] V_b [mM_per_second] Keq [dimensionless] Km_S1 [mM] Km_S2 [mM] Km_P1 [mM] Km_P2 [mM] Ki_S1 [mM] Ki_P2 [mM]
Mechanisms BiBiRev

SpecificActivationIrrev

(Validation Errors: 0) J [mM_per_second] S [mM] A [mM] V [mM_per_second] Km_S [mM] Km_A [mM]
Mechanisms UniUniIrrev_A UniBiIrrev_A UniNullIrrev_A

SpecificActivationRev

(Validation Errors: 0) J [mM_per_second] S [mM] P [mM] A [mM] V_f [mM_per_second] V_b [mM_per_second] Km_S [mM] Km_P [mM] Km_A [mM]
Mechanisms UniUniRev_A

SubstrateActivationIrrev

(Validation Errors: 0) J [mM_per_second] S [mM] V [mM_per_second] K_sa [mM] K_sc [mM]
Mechanisms UniNullIrrev UniUniIrrev UniBiIrrev

SubstrateInhibitionIrrev

(Validation Errors: 0) J [mM_per_second] S [mM] V [mM_per_second] I [mM] Km_S [mM] Ki [mM]
Mechanisms UniNullIrrev UniUniIrrev UniBiIrrev

SubstrateInhibitionRev

(Validation Errors: 0) J [mM_per_second] S [mM] P [mM] V_f [mM_per_second] V_b [mM_per_second] Km_S [mM] Km_P [mM] Ki [mM]
Mechanisms UniUniRev

UncompetitiveInhibitionIrrev

(Validation Errors: 0) J [mM_per_second] S [mM] V [mM_per_second] I [mM] Km_S [mM] K_I [mM]
Mechanisms UniUniIrrev_I UniBiIrrev_I UniNullIrrev_I