Physiology

Reaction Diagram

reactionDiagram

Cross-References

Annotations

Reactions

Reactions
Name
Structure
Kinetics
Depiction
X X_synthesis env GeneralKinetics
X X_degradation env GeneralKinetics
YYp Y_phosphorylation env GeneralKinetics
YpY Y_dephosphorylation env GeneralKinetics
RRp R_phosphorylation env GeneralKinetics
RpR 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]

global

k0

0.0 [mol.s-1.l-1]

global

k1

1.0 [s-1]

Expressions for X_degradation

reaction rate

J

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

global

k2

0.01 [s-1]

global

k2_prime

10.0 [M-1.s-1]

Expressions for Y_phosphorylation

reaction rate

J

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

global

k3

0.1 [s-1]

global

Yt

1.0 [M]

global

Km3

0.01 [M]

Expressions for Y_dephosphorylation

reaction rate

J

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

global

k4

0.2 [mol.s-1.l-1]

global

Km4

0.01 [M]

Expressions for R_phosphorylation

reaction rate

J

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

global

k5

0.1 [s-1]

global

Rt

1.0 [M]

global

Km5

0.01 [M]

Expressions for R_dephosphorylation

reaction rate

J

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

global

k6

0.05 [mol.s-1.l-1]

global

Km6

0.01 [M]

Structures

Name
Type
Electrical
env Compartment (+)   (-)

env Universal ID's

env Text Annotations

Species

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

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
Annotation
Deterministic Specs - Species
Specs - Reaction
Simulations 		Deterministic (ODE) Compartmental

Deterministic Universal ID's

Deterministic Text Annotations

Specifications (Species) - Deterministic go to Simulations

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

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

Assignments

Name Variable Assignment Function Expression
assignmentRule0 R (Rt - Rp)
assignmentRule1 Y (Yt - Yp)

Events

Name Trigger Type Variable Assignment

Geometry Compartmental2140009053

(Origin: 0.0, 0.0, 0.0; Extent: 10.0, 10.0, 10.0 [m])

Dimension Type Subdomain Adjacent Subvolumes Size Mapped Compartment
Compartmental Compartment env

Events

Name Variable Rate Expression

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

Model Format
Model Downloads
Virtual Cell Markup Language VCML File
PDF Report Report
COMBINE Archive OMEX File
SEDML SEDML File
File Format
Application Downloads
BNGL Deterministic.bngl
SBML Deterministic.sbml
Matlab Deterministic.m
NFSim XML Deterministic.xml