Physiology

Reaction Diagram

reactionDiagram

Cross-References

Annotations

Reactions

Reactions
Name
Structure
Kinetics
R R_synthesis env GeneralKinetics
R R_degradation env GeneralKinetics
Ep E E_dephosphorylation env GeneralKinetics
E Ep E_phosphorylation env GeneralKinetics

Reaction Name: R_synthesis

Universal ID's

Text Annotations

Reaction Name: R_degradation

Universal ID's

Text Annotations

Reaction Name: E_dephosphorylation

Universal ID's

Text Annotations

Reaction Name: E_phosphorylation

Universal ID's

Text Annotations

Reaction Name: R_synthesis

Expressions

reaction rate

(k0 * E) [mol.litre-1.s-1]

Reaction Name: R_degradation

Expressions

reaction rate

(k2 * R * S) [mol.litre-1.s-1]

Reaction Name: E_dephosphorylation

Expressions

reaction rate

(k3 * Ep / (Km3 + Ep)) [mol.litre-1.s-1]

Reaction Name: E_phosphorylation

Expressions

reaction rate

(k4 * R * E / (Km4 + E)) [mol.litre-1.s-1]

Structures

Name
Type
Electrical
env Compartment (+)   (-)

Structure Name: env

Universal ID's

Text Annotations

Species

Name
Structure
R env
S env
Ep env
E env

Species Name: R

Universal ID's

Text Annotations

Species Name: S

Universal ID's

Text Annotations

Species Name: Ep

Universal ID's

Text Annotations

Species Name: E

Universal ID's

Text Annotations

Molecules

Name
Description
R R ()
S S ()
E E ( mod ~P ~U )

Molucule Name: R

Universal ID's

Text Annotations

Molucule Name: S

Universal ID's

Text Annotations

Molucule Name: E

Universal ID's

Text Annotations

Observables

Name
Domain
Molecular Type
Sequence Type
O0_R_tot Molecules R Multimolecular
O0_S_tot Molecules S Multimolecular
O0_E_tot Molecules E Multimolecular

Observables Name: O0_R_tot

Universal ID's

Text Annotations

Observables Name: O0_S_tot

Universal ID's

Text Annotations

Observables Name: O0_E_tot

Universal ID's

Text Annotations

Applications

Name
Properties Math Type
Deterministic Specs - Species
Specs - Reaction
Simulations

Application Name: Deterministic

Text Annotations

Annotations will come here

Universal ID's

RFID | pubmed

Specifications (Species) - Deterministic go to Simulations

Species
Initial Condition
Diffusion Constant
R 0.0 0.0
S 0.0 0.0
Ep (Et - E) 0.0
E (Et * ((2.0 * k3 * J4) / (((k4 * R) - k3) + (J3 * (k4 * R)) + (J4 * k3) + pow((pow((((k4 * R) - k3) + (J3 * (k4 * R)) + (J4 * k3)),2.0) - (4.0 * ((k4 * R) - k3) * k3 * J4)),(1.0 / 2.0))))) 0.0

Specifications (Reaction) - Deterministic go to Simulations

Name
Enabled?
R_synthesis included
R_degradation included
E_dephosphorylation included
E_phosphorylation included

Simulations - Deterministic go to Specifications

Name
End Time
Output Options
Simulation0 1.0 every

Simulation Name: Simulation0

Universal ID's

Text Annotations

Global Parameters

Name
Expression
k0 1.0[s-1]
k2 1.0[M-1.s-1]
k3 0.5[mol.s-1.l-1]
J3 0.01[1]
k4 1.0[s-1]
J4 0.01[1]
Et 1.0[M]
Km3 (J3 * Et)[M]
Km4 (J4 * Et)[M]

Global Parameter Name: k0

Universal ID's

Text Annotations

Global Parameter Name: k2

Universal ID's

Text Annotations

Global Parameter Name: k3

Universal ID's

Text Annotations

Global Parameter Name: J3

Universal ID's

Text Annotations

Global Parameter Name: k4

Universal ID's

Text Annotations

Global Parameter Name: J4

Universal ID's

Text Annotations

Global Parameter Name: Et

Universal ID's

Text Annotations

Global Parameter Name: Km3

Universal ID's

Text Annotations

Global Parameter Name: Km4

Universal ID's

Text Annotations

Downloads

Format
File
BNGL
Metlab
SBML
Formatted XML
SEDML
Deterministic XML