Physiology
Reaction Diagram
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]
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
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
Specifications (Reaction) - Deterministic go to Simulations
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 |