Location: Metabolic Component Library @ e0e2c28e2dfd / html / MCL.html

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Metabolic Component Library(MCL)

Two of the great challenges in the mathematical modelling of biological systems are the reuse of model components, thereby allowing the combination of model parts and models, and the annotation of model components to ontologiesproviding additional level of information. We present the Metabolic Component Library (MCL), the first library of reusable and annotated model components for the modelling of metabolic metabolic networks. MCL is implemented in CellML, an XML based markup language to store and exchange mathematical models. 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.
Key features are Large set of standard reaction components for metabolic modelling Annotation of components to multiple ontologies Usage examples and re-implemented published models
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.
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.

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