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).

Naming Conventions

Substrate is named S (S1, S2, ... in case of multiple substrates)
Products is named P (P1, P2, ... in case of multiple productes)
Inhibitor is named I (I1, I2, ...)
Activator is named A (A1, A2, ...)
Modifier is named M (M1, M2, ...)
Km values are subscripted with the respective substrates or products (P -> Km_P, S -> Km_S, P1 -> Km_P1, ...)
Analog convention for inhibition constants Ki and activation constants Ka.

Units

Time: second
Volume Unit: liter
Quantity Unit: mmol

Components

AllostericInhibitionEmpirical

CellML
AllostericInhibitionEmpirical
UniUniRev_I

AllostericInhibitionMWC

CellML
AllostericInhibitionMWC
UniUniIrrev_I UniBiIrrev_I UniNullIrrev_I

BiIrrev

CellML
BiIrrev
BiNullIrrev BiBiIrrev BiUniIrrev

CatalyticActivationIrrev

CellML
CatalyticActivationIrrev
UniUniIrrev_A UniBiIrrev_A UniNullIrrev_A

CatalyticActivationRev

CellML
CatalyticActivationRev
UniUniRev_A

CompetitiveInhibitionIrrev

CellML
CompetitiveInhibitionIrrev
UniUniIrrev_I UniBiIrrev_I UniNullIrrev_I

CompetitiveInhibitionRev

CellML
CompetitiveInhibitionRev
UniUniRev_I

ConstantFluxIrrev

CellML
ConstantFluxIrrev
UniNullIrrev UniUniIrrev UniBiIrrev BiBiIrrev BiUniIrrev

Hill1ModifierRev

CellML
Hill1ModifierRev
UniUniRev_M

Hill2ModifierRev

CellML
Hill2ModifierRev
UniUniRev_M2

HillIrrev

CellML
HillIrrev
UniNullIrrev UniUniIrrev UniBiIrrev

HillRev

CellML
HillRev
UniUniRev

HyperbolicModifierIrrev

CellML
HyperbolicModifierIrrev
UniNullIrrev_M UniUniIrrev_M UniBiIrrev_M

HyperbolicModifierRev

CellML
HyperbolicModifierRev
UniUniRev_M

IsoUniUni

CellML
IsoUniUni
UniUniRev

MassActionBiBiRev

CellML
MassActionBiBiRev
BiBiRev BiBiRev

MassActionBiIrrev

CellML
MassActionBiIrrev
BiNullIrrev BiBiIrrev BiUniIrrev

MassActionBiUniRev

CellML
MassActionBiUniRev
BiUniRev

MassActionUniBiRev

CellML
MassActionUniBiRev
UniBiRev

MassActionUniIrrev

CellML
MassActionUniIrrev
UniNullIrrev UniUniIrrev UniBiIrrev

MassActionUniUniRev

CellML
MassActionUniUniRev
UniUniRev

MichaelisMentenIrrev

CellML
MichaelisMentenIrrev
UniNullIrrev UniUniIrrev UniBiIrrev

MichaelisMentenRev

CellML
MichaelisMentenRev
UniUniRev

MixedActivationIrrev

CellML
MixedActivationIrrev
UniUniIrrev_A UniBiIrrev_A UniNullIrrev_A

MixedActivationRev

CellML
MixedActivationRev
UniUniRev_A

MixedInhibitionIrrev

CellML
MixedInhibitionIrrev
UniUniIrrev_I UniBiIrrev_I UniNullIrrev_I

MixedInhibitionRev

CellML
MixedInhibitionRev
UniUniRev_I

NoncompetitiveInhibitionIrrev

CellML
NoncompetitiveInhibitionIrrev
UniUniIrrev_I UniBiIrrev_I UniNullIrrev_I

NoncompetitiveInhibitionRev

CellML
NoncompetitiveInhibitionRev
UniUniRev_I

OrderedBiBi

CellML
OrderedBiBi
BiBiRev BiBiRev

OrderedBiUni

CellML
OrderedBiUni
BiUniRev

OrderedUniBi

CellML
OrderedUniBi
UniBiRev

PingPongBiBi

CellML
PingPongBiBi
BiBiRev BiBiRev

SpecificActivationIrrev

CellML
SpecificActivationIrrev
UniUniIrrev_A UniBiIrrev_A UniNullIrrev_A

SpecificActivationRev

CellML
SpecificActivationRev
UniUniRev_A

SubstrateActivationIrrev

CellML
SubstrateActivationIrrev
UniNullIrrev UniUniIrrev UniBiIrrev

SubstrateInhibitionIrrev

CellML
SubstrateInhibitionIrrev
UniNullIrrev UniUniIrrev UniBiIrrev

SubstrateInhibitionRev

CellML
SubstrateInhibitionRev
UniUniRev

UncompetitiveInhibitionIrrev

CellML
UncompetitiveInhibitionIrrev
UniUniIrrev_I UniBiIrrev_I UniNullIrrev_I