Library of metabolic components in 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

AllostericInhibitionMWC

BiIrrev

CatalyticActivationIrrev

CatalyticActivationRev

CompetitiveInhibitionIrrev

CompetitiveInhibitionRev

ConstantFlux

HenriMichaelisMentenIrrev

HillCooperativity

HyperbolicModifierIrrev

HyperbolicModifierRev

IsoUniUni

MassActionBiBiRev

MassActionBiIrrev

MassActionBiUniRev

MassActionUniBiRev

MassActionUniIrrev

MassActionUniUniRev

MixedActivationIrrev

MixedActivationRev

MixedInhibitionIrrev

MixedInhibitionRev

NoncompetitiveInhibitionIrrev

NoncompetitiveInhibitionRev

OrderedBiBi

OrderedBiUni

OrderedUniBi

PingPongBiBi

ReversibleHill

ReversibleHill1Modifier

ReversibleHill2Modifier

ReversibleMichaelisMenten

SpecificActivationIrrev

SpecificActivationRev

SubstrateActivationIrrev

SubstrateInhibitionIrrev

SubstrateInhibitionRev

UncompetitiveInhibitionIrrev

UncompetitiveInhibitionRev

UniUni

Source
Derived from workspace Metabolic Component Library at changeset a0b670aa4a20.
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