Physiology

Reaction Diagram

reactionDiagram

Cross-References

Annotations

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

X_synthesis Universal ID's

X_synthesis Text Annotations

X_degradation Universal ID's

X_degradation Text Annotations

Y_phosphorylation Universal ID's

Y_phosphorylation Text Annotations

Y_dephosphorylation Universal ID's

Y_dephosphorylation Text Annotations

R_phosphorylation Universal ID's

R_phosphorylation Text Annotations

R_dephosphorylation Universal ID's

R_dephosphorylation Text Annotations

Expressions for X_synthesis

reaction rate

J

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

Expressions for X_degradation

reaction rate

J

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

Expressions for Y_phosphorylation

reaction rate

J

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

Expressions for Y_dephosphorylation

reaction rate

J

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

Expressions for R_phosphorylation

reaction rate

J

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

Expressions for R_dephosphorylation

reaction rate

J

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

Structures

Name
Type
Electrical
env Compartment (+)   (-)

env Universal ID's

env Text Annotations

Species

Name
Structure
BioNetGen Definition
Depiction
Rp env R(mod~P!-,).
X env X().
Yp env Y(mod~P!-,).
S env S().
Y env Y(mod~U!-,).
R env R(mod~U!-,).

Rp Universal ID's

Rp Text Annotations

X Universal ID's

X Text Annotations

Yp Universal ID's

Yp Text Annotations

S Universal ID's

S Text Annotations

Y Universal ID's

Y Text Annotations

R Universal ID's

R Text Annotations

Molecules

Name
BioNetGen Definition
DEPICTION
R R(mod~P~U,)
X X()
Y Y(mod~P~U,)
S S()

R Universal ID's

R Text Annotations

X Universal ID's

X Text Annotations

Y Universal ID's

Y Text Annotations

S Universal ID's

S Text Annotations

Observables

Name
Structure
Count
BNGL Definition
Sequence Type
DEPICTION
O0_R_tot env Molecules R(mod!?,). Multimolecular
O0_X_tot env Molecules X(). Multimolecular
O0_Y_tot env Molecules Y(mod!?,). Multimolecular
O0_S_tot env Molecules S(). Multimolecular

O0_R_tot Universal ID's

O0_R_tot Text Annotations

O0_X_tot Universal ID's

O0_X_tot Text Annotations

O0_Y_tot Universal ID's

O0_Y_tot Text Annotations

O0_S_tot Universal ID's

O0_S_tot Text Annotations

Applications

Name
Properties Math Type
Deterministic Specs - Species
Specs - Reaction
Simulations 		Deterministic (ODE) Compartmental

Deterministic Text Annotations

Deterministic Universal ID's

Annotations will come here

RFID | pubmed

Specifications (Species) - Deterministic go to Simulations

Species
Initial Condition
Diffusion Constant
Rp 0.0 0.0 [m2/s]
X 0.0 0.0 [m2/s]
Yp 0.0 0.0 [m2/s]
S 0.0 0.0 [m2/s]
Y (Yt - Yp) 0.0 [m2/s]
R (Rt - Rp) 0.0 [m2/s]

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

KeepEvery 1

KeepAtMost 1000

Deterministic Universal ID's

Deterministic Text Annotations

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]

Universal ID's

Text Annotations

Universal ID's

Text Annotations

Universal ID's

Text Annotations

Universal ID's

Text Annotations

Universal ID's

Text Annotations

Universal ID's

Text Annotations

Universal ID's

Text Annotations

Universal ID's

Text Annotations

Universal ID's

Text Annotations

Universal ID's

Text Annotations

Universal ID's

Text Annotations

Universal ID's

Text Annotations

Universal ID's

Text Annotations

Universal ID's

Text Annotations

Downloads

Format
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BNGL
MatLab
SBML
Formatted XML
SEDML