Reaction Diagram
Physiology
| Universal ID's | Text Annotations |
|---|---|
|
|
|
| Reaction |
Name
Structure
|
Kinetics | Depiction |
|---|---|---|---|
| GEFActive_GEF |
GEF_activation
default
|
GeneralKinetics | GEFActive_GEF |
|
|
|
reaction rate (J): (Activator * GEF * k1)[umol.l-1.min-1]
|
|
| Active_GEFGEF |
GEF_inactivation
default
|
GeneralKinetics | Active_GEFGEF |
|
|
|
reaction rate (J): (Active_GEF * k2)[umol.l-1.min-1]
|
|
| Activator |
Activator_degradation
default
|
GeneralKinetics | Activator |
|
|
|
reaction rate (J): (Activator * k3)[umol.l-1.min-1]
|
| Name |
Type
Electrical (Membrane Polarity)
|
|---|---|
| default |
Compartment
(+) (-)
|
|
|
|
| Name | Structure | BioNetGen Definition |
|---|---|---|
| Activator | default | Activator(). |
|
|
|
|
| GEF | default | RhoGEF(Active~no!-,). |
|
|
|
|
| Active_GEF | default | RhoGEF(Active~yes!-,). |
|
|
|
| Name | Text Annotations | BioNetGen Definition |
|---|---|---|
| Activator | Text Annotations | Activator() |
|
|
|
|
| RhoGEF | Text Annotations | RhoGEF(Active~no~yes,) |
|
|
|
| Name |
Type
Count
|
BioNetGen Definition |
|---|---|---|
| O0_Activator_tot |
Molecules Multimolecular |
Activator(). |
|
|
|
|
| O0_RhoGEF_tot |
Molecules Multimolecular |
RhoGEF(Active!?,). |
|
|
|
Applications
| Name | Math Type | Annotation |
|---|---|---|
| Canonical Application | Deterministic (ODE) Compartmental |
Application - Canonical Application
| Species | Initial Condition | Diffusion Constant | ||||||
|---|---|---|---|---|---|---|---|---|
| Activator | 1.0 [umol] | 0.0
[m2/min] | GEF |
0.31
[umol]
|
0.0
[m2/min] | Active_GEF |
0.0
[umol]
|
0.0
[m2/min]
|
|
| Name | Reaction Mapping |
|---|---|
| GEF_activation | included |
| GEF_inactivation | included |
| Activator_degradation | included |
| Name | End Time | Output Options |
|---|---|---|
| Simulation0 | 600.0 [min] |
KeepEvery 1 KeepAtMost 1000 |
| Dimension | Type | Subdomain | Adjacent Subvolumes | Size | Mapped Compartment |
|---|---|---|---|---|---|
| Compartmental | Compartment | default |
Global Parameters
| Name | Expression |
|---|---|
| k3 | 0.5[min-1] |
|
|
|
| k2 | 0.1[min-1] |
|
|
|
| kcatGEF | 5.64[min-1] |
|
|
|
| KmGEFRho | 24.5[umol.l-1] |
|
|
|
| KmGEFGDI | 1.0[umol.l-1] |
|
|
|
| k1 | 1.0[l.umol-1.min-1] |
|
|
|