MCL-v0.1.cellml
MCL TutorialMetabolic Component Library(MCL)
| We present the Metabolic Component Library (MCL), an open-source library for the modelling of metabolic components and metabolic networks in CellML. | 
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Key features are
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| MCL was developed by Matthias König at the Charité Berlin with support from Randall Britten from the Auckland Bioengineering Institute and Maxwell Neal from the University of Washington. |
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| Annotation of the metabolic components to biological ontologies was performed with SemGen developed by Dr. Maxwell Neal at the University of Washington. |
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| The project was funded by the Virtual Liver Network (VLN). |  |
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Please try and report any questions or problems to
matthias.koenig[AT]charite.de Thanks and have fun The MCL team. |
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
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(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] |
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Mechanisms UniUniRev_I |
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AllostericInhibitionMWC
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(Validation Errors: 1) J [mM_per_second] S [mM] I [mM] V [mM_per_second] Km_S [mM] n [dimensionless] L [dimensionless] Ki [mM] |
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Mechanisms UniUniIrrev_I UniBiIrrev_I UniNullIrrev_I |
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BiIrrev
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(Validation Errors: 0) J [mM_per_second] S1 [mM] S2 [mM] V [mM_per_second] Km_S1 [mM] Km_S2 [mM] |
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Mechanisms BiNullIrrev BiBiIrrev BiUniIrrev |
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CatalyticActivationIrrev
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(Validation Errors: 0) J [mM_per_second] S [mM] A [mM] V [mM_per_second] Km_S [mM] Km_A [mM] |
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Mechanisms UniUniIrrev_A UniBiIrrev_A UniNullIrrev_A |
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CatalyticActivationRev
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(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] |
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Mechanisms UniUniRev_A |
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CompetitiveInhibitionIrrev
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(Validation Errors: 0) J [mM_per_second] S [mM] I [mM] V [mM_per_second] Km_S [mM] Ki [mM] |
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Mechanisms UniUniIrrev_I UniBiIrrev_I UniNullIrrev_I |
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CompetitiveInhibitionRev
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(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] |
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Mechanisms UniUniRev_I |
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ConstantFluxIrrev
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(Validation Errors: 0) J [mM_per_second] V [mM_per_second] |
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Mechanisms UniNullIrrev UniUniIrrev UniBiIrrev BiBiIrrev BiUniIrrev |
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Hill1ModifierRev
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(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] |
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Mechanisms UniUniRev_M |
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Hill2ModifierRev
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(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] |
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Mechanisms UniUniRev_M2 |
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HillIrrev
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(Validation Errors: 1) J [mM_per_second] S [mM] V [mM_per_second] Km_S [mM] n [dimensionless] |
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Mechanisms UniNullIrrev UniUniIrrev UniBiIrrev |
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HillRev
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(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] |
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Mechanisms UniUniRev |
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HyperbolicModifierIrrev
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(Validation Errors: 0) J [mM_per_second] S [mM] M [mM] V [mM_per_second] Kd [mM] Km_S [mM] a [dimensionless] b [dimensionless] |
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Mechanisms UniNullIrrev_M UniUniIrrev_M UniBiIrrev_M |
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HyperbolicModifierRev
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(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] |
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Mechanisms UniUniRev_M |
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IsoUniUni
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(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] |
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Mechanisms UniUniRev |
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MassActionBiBiRev
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(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] |
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Mechanisms BiBiRev |
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MassActionBiIrrev
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(Validation Errors: 0) J [mM_per_second] S1 [mM] S2 [mM] k_f [per_mM_per_second] |
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Mechanisms BiNullIrrev BiBiIrrev BiUniIrrev |
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MassActionBiUniRev
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(Validation Errors: 0) J [mM_per_second] S1 [mM] S2 [mM] P [mM] k_f [per_mM_per_second] k_b [per_second] |
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Mechanisms BiUniRev |
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MassActionUniBiRev
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(Validation Errors: 0) J [mM_per_second] S [mM] P1 [mM] P2 [mM] k_f [per_second] k_b [per_mM_per_second] |
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Mechanisms UniBiRev |
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MassActionUniIrrev
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(Validation Errors: 0) J [mM_per_second] S [mM] k_f [per_second] |
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Mechanisms UniNullIrrev UniUniIrrev UniBiIrrev |
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MassActionUniUniRev
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(Validation Errors: 0) J [mM_per_second] S [mM] P [mM] k_f [per_second] k_b [per_second] |
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Mechanisms UniUniRev |
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MichaelisMentenIrrev
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(Validation Errors: 0) J [mM_per_second] S [mM] V [mM_per_second] Km_S [mM] |
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Mechanisms UniNullIrrev UniUniIrrev UniBiIrrev |
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MichaelisMentenRev
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(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] |
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Mechanisms UniUniRev |
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MixedActivationIrrev
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(Validation Errors: 0) J [mM_per_second] S [mM] A [mM] V [mM_per_second] Kac [mM] Kas [mM] Km_S [mM] |
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Mechanisms UniUniIrrev_A UniBiIrrev_A UniNullIrrev_A |
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MixedActivationRev
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(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] |
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Mechanisms UniUniRev_A |
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MixedInhibitionIrrev
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(Validation Errors: 0) J [mM_per_second] S [mM] I [mM] V [mM_per_second] Kis [mM] Kic [mM] Km_S [mM] |
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Mechanisms UniUniIrrev_I UniBiIrrev_I UniNullIrrev_I |
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MixedInhibitionRev
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(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] |
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Mechanisms UniUniRev_I |
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NoncompetitiveInhibitionIrrev
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(Validation Errors: 0) J [mM_per_second] S [mM] V [mM_per_second] Km_S [mM] I [mM] Ki [mM] |
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Mechanisms UniUniIrrev_I UniBiIrrev_I UniNullIrrev_I |
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NoncompetitiveInhibitionRev
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(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] |
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Mechanisms UniUniRev_I |
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OrderedBiBi
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(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] |
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Mechanisms BiBiRev |
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OrderedBiUni
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(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] |
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Mechanisms BiUniRev |
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OrderedUniBi
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(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] |
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Mechanisms UniBiRev |
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PingPongBiBi
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(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] |
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Mechanisms BiBiRev |
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SpecificActivationIrrev
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(Validation Errors: 0) J [mM_per_second] S [mM] A [mM] V [mM_per_second] Km_S [mM] Km_A [mM] |
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Mechanisms UniUniIrrev_A UniBiIrrev_A UniNullIrrev_A |
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SpecificActivationRev
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(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] |
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Mechanisms UniUniRev_A |
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SubstrateActivationIrrev
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(Validation Errors: 0) J [mM_per_second] S [mM] V [mM_per_second] K_sa [mM] K_sc [mM] |
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Mechanisms UniNullIrrev UniUniIrrev UniBiIrrev |
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SubstrateInhibitionIrrev
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(Validation Errors: 0) J [mM_per_second] S [mM] V [mM_per_second] I [mM] Km_S [mM] Ki [mM] |
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Mechanisms UniNullIrrev UniUniIrrev UniBiIrrev |
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SubstrateInhibitionRev
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(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] |
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Mechanisms UniUniRev |
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UncompetitiveInhibitionIrrev
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(Validation Errors: 0) J [mM_per_second] S [mM] V [mM_per_second] I [mM] Km_S [mM] K_I [mM] |
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Mechanisms UniUniIrrev_I UniBiIrrev_I UniNullIrrev_I |
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