Reaction Diagram
Physiology
| Universal ID's | Text Annotations |
|---|---|
|
|
|
| Reaction |
Name
Structure
|
Kinetics | Depiction |
|---|---|---|---|
| MekMek_act |
Mek_Activation
cell
|
GeneralKinetics | MekMek_act |
|
|
|
reaction rate (J): (Kcat * Raf1_act * Mek / (km + Mek))[mmol.ml-1.min-1]
user defined (km): 4768350.0[mmol.ml-1] user defined (Kcat): 185.759[min-1] |
|
| Mek_actMek |
Mek_Deactivation
cell
|
GeneralKinetics | Mek_actMek |
|
|
|
reaction rate (J): (Kcat * PP2A_act * Mek_act / (km + Mek_act))[mmol.ml-1.min-1]
user defined (km): 518753.0[mmol.ml-1] user defined (Kcat): 2.83243[min-1] |
|
| MekMek_act |
Mek_Activation_bRaf
cell
|
GeneralKinetics | MekMek_act |
|
|
|
reaction rate (J): (kcat * bRaf_act * Mek / (km + Mek))[mmol.ml-1.min-1]
user defined (km): 4768350.0[mmol.ml-1] user defined (kcat): 185.759[min-1] |
| Name |
Type
Electrical (Membrane Polarity)
|
|---|---|
| cell |
Compartment
(+) (-)
|
|
|
|
| Name | Structure | BioNetGen Definition |
|---|---|---|
| Raf1_act | cell | Raf(Active~yes!-,). |
|
|
|
|
| Mek_act | cell | MEK(Active~yes!-,). |
|
|
|
|
| Mek | cell | MEK(Active~no!-,). |
|
|
|
|
| bRaf_act | cell | B_Raf(Active~yes!-,). |
|
|
|
|
| PP2A_act | cell | PP2A(Active~yes!-,). |
|
|
|
| Name | Text Annotations | BioNetGen Definition |
|---|---|---|
| Raf | Text Annotations | Raf(Active~yes~no,) |
|
|
|
|
| MEK | Text Annotations | MEK(Active~yes~no,) |
|
|
|
|
| B_Raf | Text Annotations | B_Raf(Active~yes~no,) |
|
|
|
|
| PP2A | Text Annotations | PP2A(Active~yes~no,) |
|
|
|
| Name |
Type
Count
|
BioNetGen Definition |
|---|
Applications
| Name | Math Type | Annotation |
|---|---|---|
| Deterministic | Deterministic (ODE) Compartmental | cloned from 'Deterministic' owned by user savi06 cloned from 'Deterministic' owned by user mblinov cloned from 'Deterministic' owned by user cab15130 |
Application - Deterministic
| Species | Initial Condition | Diffusion Constant | ||||||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
| Raf1_act | (1800.0 * (t > 1.0) * (t < 3.0)) [mmol] | 0.0
[m2/min] | Mek_act |
0.0
[mmol]
|
0.0
[m2/min] | Mek |
600000.0
[mmol]
|
0.0
[m2/min] | bRaf_act |
(14000.0 * (t > 1.0) * (t < 7.0))
[mmol]
|
0.0
[m2/min] | PP2A_act |
120000.0
[mmol]
|
0.0
[m2/min]
|
|
| Name | Reaction Mapping |
|---|---|
| Mek_Activation | included |
| Mek_Deactivation | included |
| Mek_Activation_bRaf | included |
| Name | End Time | Output Options |
|---|---|---|
| Simulation0 | 10.0 [min] |
KeepEvery 1 KeepAtMost 1000 |
| Name | Variable | Assignment Function Expression |
|---|---|---|
| assignmentRule0 | Raf1_act | (1800.0 * (t > 1.0) * (t < 3.0)) |
| assignmentRule1 | bRaf_act | (14000.0 * (t > 1.0) * (t < 7.0)) |
| Dimension | Type | Subdomain | Adjacent Subvolumes | Size | Mapped Compartment |
|---|---|---|---|---|---|
| Compartmental | Compartment | cell |
Global Parameters
| Name | Expression |
|---|