Metabolic Component Library(MCL)
Two of the great challenges in the mathematical modelling of biological systems are
The library covers among others the full set of function definitions for processes from COPASI 4.8 (Bulid 35) as well as standard simplified kinetics like mass action kinetics. |
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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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The project was funded by the Virtual Liver Network (VLN). Please try and report any questions or problems to matthias.koenigcharite.de Thanks and have fun The MCL team. |
Examples
Usage examples of the MCL: TODO
Annotations
All components in the SBML are annotated to the Systems Biology Ontology (SBO) and the The Ontology of Physics for Biology (OPB). The example models are furthermore annotated to biological databased like the Gene Ontology, KEGG and ChEBI. | |
Annotation of the metabolic components to biological ontologies was performed with
SemGen developed
by Dr. Maxwell Neal at the University of Washington. The annotations are distributed in OWL format with the MCL and the MCL examples and can be read with SemGen. |
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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] |
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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] |
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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] |
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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] |
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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] |
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Mechanisms UniUniRev_A |
CompetitiveInhibitionIrrev
(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 |
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] |
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Mechanisms UniUniRev_I |
ConstantFluxIrrev
(Validation Errors: 0) J [mM_per_second] V [mM_per_second] |
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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] |
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Mechanisms UniUniRev_M |
Hill2ModifierRev
HillIrrev
(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 |
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] |
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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] |
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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] |
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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] |
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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] |
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Mechanisms BiBiRev |
MassActionBiIrrev
(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 |
MassActionBiUniRev
(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 |
MassActionUniBiRev
(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 |
MassActionUniIrrev
(Validation Errors: 0) J [mM_per_second] S [mM] k_f [per_second] |
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Mechanisms UniNullIrrev UniUniIrrev UniBiIrrev |
MassActionUniUniRev
(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 |
MichaelisMentenIrrev
(Validation Errors: 0) J [mM_per_second] S [mM] V [mM_per_second] Km_S [mM] |
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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] |
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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] |
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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] |
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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] |
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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] |
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Mechanisms UniUniRev_I |
NoncompetitiveInhibitionIrrev
(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 |
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] |
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Mechanisms UniUniRev_I |
OrderedBiBi
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] |
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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] |
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Mechanisms UniBiRev |
PingPongBiBi
SpecificActivationIrrev
(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 |
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] |
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Mechanisms UniUniRev_A |
SubstrateActivationIrrev
(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 |
SubstrateInhibitionIrrev
(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 |
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] |
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Mechanisms UniUniRev |
UncompetitiveInhibitionIrrev
(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 |