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Author:

Matthias K?nig <matthias.koenig@charite.de>

Date:

2013-04-09 15:08:59+02:00

Desc:

Documentation of Reaction Mechanism. Images for basic mechanisms created.

Permanent Source URI:

https://staging.physiomeproject.org/w/matthiaskoenig/MetabolicComponentLibrary/rawfile/af10084679bb928d763a8ff441ed93d41aa59126/components.html

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

UniUniRev_I  

---

AllostericInhibitionMWC

CellML

UniUniIrrev_I   UniBiIrrev_I   UniNullIrrev_I  

---

BiIrrev

CellML

BiNullIrrev   BiBiIrrev   BiUniIrrev  

---

CatalyticActivationIrrev

CellML

UniUniIrrev_A   UniBiIrrev_A   UniNullIrrev_A  

---

CatalyticActivationRev

CellML

UniUniRev_A  

---

CompetitiveInhibitionIrrev

CellML

UniUniIrrev_I   UniBiIrrev_I   UniNullIrrev_I  

---

CompetitiveInhibitionRev

CellML

UniUniRev_I  

---

ConstantFluxIrrev

CellML

UniNullIrrev   UniUniIrrev   UniBiIrrev   BiBiIrrev   BiUniIrrev  

---

Hill1ModifierRev

CellML

UniUniRev_M  

---

Hill2ModifierRev

CellML

UniUniRev_M2  

---

HillIrrev

CellML

UniNullIrrev   UniUniIrrev   UniBiIrrev  

---

HillRev

CellML

UniUniRev  

---

HyperbolicModifierIrrev

CellML

UniNullIrrev_M   UniUniIrrev_M   UniBiIrrev_M  

---

HyperbolicModifierRev

CellML

UniUniRev_M  

---

IsoUniUni

CellML

UniUniRev  

---

MassActionBiBiRev

CellML

BiBiRev  

---

MassActionBiIrrev

CellML

BiNullIrrev   BiBiIrrev   BiUniIrrev  

---

MassActionBiUniRev

CellML

BiUniRev  

---

MassActionUniBiRev

CellML

UniBiRev  

---

MassActionUniIrrev

CellML

UniNullIrrev   UniUniIrrev   UniBiIrrev  

---

MassActionUniUniRev

CellML

UniUniRev  

---

MichaelisMentenIrrev

CellML

UniNullIrrev   UniUniIrrev   UniBiIrrev  

---

MichaelisMentenRev

CellML

UniUniRev  

---

MixedActivationIrrev

CellML

UniUniIrrev_A   UniBiIrrev_A   UniNullIrrev_A  

---

MixedActivationRev

CellML

UniUniRev_A  

---

MixedInhibitionIrrev

CellML

UniUniIrrev_I   UniBiIrrev_I   UniNullIrrev_I  

---

MixedInhibitionRev

CellML

UniUniRev_I  

---

NoncompetitiveInhibitionIrrev

CellML

UniUniIrrev_I   UniBiIrrev_I   UniNullIrrev_I  

---

NoncompetitiveInhibitionRev

CellML

UniUniRev_I  

---

OrderedBiBi

CellML

BiBiRev  

---

OrderedBiUni

CellML

BiUniRev  

---

OrderedUniBi

CellML

UniBiRev  

---

PingPongBiBi

CellML

BiBiRev  

---

SpecificActivationIrrev

CellML

UniUniIrrev_A   UniBiIrrev_A   UniNullIrrev_A  

---

SpecificActivationRev

CellML

UniUniRev_A  

---

SubstrateActivationIrrev

CellML

UniNullIrrev   UniUniIrrev   UniBiIrrev  

---

SubstrateInhibitionIrrev

CellML

UniNullIrrev   UniUniIrrev   UniBiIrrev  

---

SubstrateInhibitionRev

CellML

UniUniRev  

---

UncompetitiveInhibitionIrrev

CellML

UniUniIrrev_I   UniBiIrrev_I   UniNullIrrev_I  

---