Physiology

Reaction Diagram

reactionDiagram

Cross-References

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Reactions

Reactions
Name
Structure
Kinetics
X X_synthesis env GeneralKinetics
X X_degradation env GeneralKinetics
Y Yp Y_phosphorylation env GeneralKinetics
Yp Y Y_dephosphorylation env GeneralKinetics
R Rp R_phosphorylation env GeneralKinetics
Rp R R_dephosphorylation env GeneralKinetics

Reaction Name: X_synthesis

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Reaction Name: X_degradation

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Reaction Name: Y_phosphorylation

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Reaction Name: Y_dephosphorylation

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Reaction Name: R_phosphorylation

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Reaction Name: R_dephosphorylation

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Reaction Name: X_synthesis

Expressions

reaction rate

(k0 + (k1 * S)) [mol.litre-1.s-1]

Reaction Name: X_degradation

Expressions

reaction rate

((k2 + (k2_prime * Rp)) * X) [mol.litre-1.s-1]

Reaction Name: Y_phosphorylation

Expressions

reaction rate

(k3 * X * (Yt - Yp) / (Km3 + Yt - Yp)) [mol.litre-1.s-1]

Reaction Name: Y_dephosphorylation

Expressions

reaction rate

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

Reaction Name: R_phosphorylation

Expressions

reaction rate

(k5 * Yp * (Rt - Rp) / (Km5 + Rt - Rp)) [mol.litre-1.s-1]

Reaction Name: R_dephosphorylation

Expressions

reaction rate

(k6 * Rp / (Km6 + Rp)) [mol.litre-1.s-1]

Structures

Name
Type
Electrical
env Compartment (+)   (-)

Structure Name: env

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Species

Name
Structure
Rp env
X env
Yp env
S env
Y env
R env

Species Name: Rp

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Species Name: X

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Species Name: Yp

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Species Name: S

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Species Name: Y

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Species Name: R

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Molecules

Name
Description
R R ( mod ~P ~U )
X X ()
Y Y ( mod ~P ~U )
S S ()

Molucule Name: R

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Molucule Name: X

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Molucule Name: Y

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Molucule Name: S

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Observables

Name
Domain
Molecular Type
Sequence Type
O0_R_tot Molecules R Multimolecular
O0_X_tot Molecules X Multimolecular
O0_Y_tot Molecules Y Multimolecular
O0_S_tot Molecules S Multimolecular

Observables Name: O0_R_tot

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Observables Name: O0_X_tot

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Observables Name: O0_Y_tot

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Observables Name: O0_S_tot

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Applications

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

Application Name: Deterministic

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Annotations will come here

Universal ID's

RFID | pubmed

Specifications (Species) - Deterministic go to Simulations

Species
Initial Condition
Diffusion Constant
Rp 0.0 0.0
X 0.0 0.0
Yp 0.0 0.0
S 0.0 0.0
Y (Yt - Yp) 0.0
R (Rt - Rp) 0.0

Specifications (Reaction) - Deterministic go to Simulations

Name
Enabled?
X_synthesis included
X_degradation included
Y_phosphorylation included
Y_dephosphorylation included
R_phosphorylation included
R_dephosphorylation included

Simulations - Deterministic go to Specifications

Name
End Time
Output Options
Simulation0 1.0 every

Simulation Name: Simulation0

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Global Parameters

Name
Expression
k0 0.0[mol.s-1.l-1]
k1 1.0[s-1]
k2 0.01[s-1]
k2_prime 10.0[M-1.s-1]
k3 0.1[s-1]
Yt 1.0[M]
Km3 0.01[M]
k4 0.2[mol.s-1.l-1]
Km4 0.01[M]
k5 0.1[s-1]
Rt 1.0[M]
Km5 0.01[M]
k6 0.05[mol.s-1.l-1]
Km6 0.01[M]

Global Parameter Name: k0

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Global Parameter Name: k1

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Global Parameter Name: k2

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Global Parameter Name: k2_prime

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Global Parameter Name: k3

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Global Parameter Name: Yt

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Global Parameter Name: Km3

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Global Parameter Name: k4

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Global Parameter Name: Km4

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Global Parameter Name: k5

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Global Parameter Name: Rt

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Global Parameter Name: Km5

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Global Parameter Name: k6

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Global Parameter Name: Km6

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Downloads

Format
File
BNGL
Metlab
SBML
Formatted XML
SEDML
Deterministic XML