Physiology
Reaction Diagram
Cross-References
Annotations
Reactions
Reactions | Name | Structure | Kinetics | Depiction |
---|---|---|---|---|
MekMek_act | Mek_Activation | cell | GeneralKinetics | |
Mek_actMek | Mek_Deactivation | cell | GeneralKinetics | |
MekMek_act | Mek_Activation_bRaf | cell | GeneralKinetics |
Mek_Activation Universal ID's
Mek_Activation Text Annotations
Mek_Deactivation Universal ID's
Mek_Deactivation Text Annotations
Mek_Activation_bRaf Universal ID's
Mek_Activation_bRaf Text Annotations
Expressions for Mek_Activation
reaction rate
J
(Kcat * Raf1_act * Mek / (km + Mek)) [mmol.ml-1.min-1]
local
km
4768350.0 [mmol.ml-1]
local
Kcat
185.759 [min-1]
Expressions for Mek_Deactivation
reaction rate
J
(Kcat * PP2A_act * Mek_act / (km + Mek_act)) [mmol.ml-1.min-1]
local
km
518753.0 [mmol.ml-1]
local
Kcat
2.83243 [min-1]
Expressions for Mek_Activation_bRaf
reaction rate
J
(kcat * bRaf_act * Mek / (km + Mek)) [mmol.ml-1.min-1]
local
km
4768350.0 [mmol.ml-1]
local
kcat
185.759 [min-1]
Species
Name | Structure | BioNetGen Definition | Depiction |
---|---|---|---|
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!-,). |
Raf1_act Universal ID's
Raf1_act Text Annotations
Mek_act Universal ID's
Mek_act Text Annotations
Mek Universal ID's
Mek Text Annotations
bRaf_act Universal ID's
bRaf_act Text Annotations
PP2A_act Universal ID's
PP2A_act Text Annotations
Molecules
Name | BioNetGen Definition | DEPICTION |
---|---|---|
Raf | Raf(Active~yes~no,) | |
MEK | MEK(Active~yes~no,) | |
B_Raf | B_Raf(Active~yes~no,) | |
PP2A | PP2A(Active~yes~no,) |
Raf Universal ID's
Raf Text Annotations
MEK Universal ID's
MEK Text Annotations
B_Raf Universal ID's
B_Raf Text Annotations
PP2A Universal ID's
PP2A Text Annotations
Applications
Name | Properties | Math Type | Annotation |
---|---|---|---|
Deterministic |
Specs -
Species Specs - Reaction Simulations |
Deterministic (ODE) Compartmental | cloned from 'Deterministic' owned by user savi06 cloned from 'Deterministic' owned by user mblinov cloned from 'Deterministic' owned by user cab15130 |
Deterministic Universal ID's
Deterministic Text Annotations
Specifications (Species) - Deterministic go to Simulations
Species | Initial Condition | Diffusion Constant | Structure |
---|---|---|---|
Raf1_act | (1800.0 * (t > 1.0) * (t < 3.0)) [mmol] | 0.0 [m2/min] | cell |
Mek_act | 0.0 [mmol] | 0.0 [m2/min] | cell |
Mek | 600000.0 [mmol] | 0.0 [m2/min] | cell |
bRaf_act | (14000.0 * (t > 1.0) * (t < 7.0)) [mmol] | 0.0 [m2/min] | cell |
PP2A_act | 120000.0 [mmol] | 0.0 [m2/min] | cell |
Specifications (Reaction) - Deterministic go to Simulations
Simulations - Deterministic go to Specifications
Name | End Time | Output Options |
---|---|---|
Simulation0 | 10.0 |
KeepEvery 1 KeepAtMost 1000 |
Deterministic Universal ID's
Deterministic Text Annotations
Assignments
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)) |
Events
Name | Trigger Type | Variable Assignment |
---|
Geometry Compartmental1162560315
(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 | cell |
Events
Name | Variable | Rate Expression |
---|
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 |