You are here: Home / User Workspace / matthiaskoenig / Metabolic Component Library

Author:

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

Date:

2013-04-10 16:39:43+02:00

Desc:

Proper encapsulation of all the example files with separation into network/reaction/librarycomponent structure. Some smaller bugfixes in mapping between components.

Permanent Source URI:

https://staging.physiomeproject.org/w/matthiaskoenig/MetabolicComponentLibrary/rawfile/ef052da4ad7bc62239ca17cec24ce736e18e1995/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).

Components

Substrate(s) : S (S1, S2, ...)
Product(s) : P (P1, P2, ... )
Inhibitor : I (I1, I2, ...)
Activator : A (A1, A2, ...)
Modifier : 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

---