Physiology
Reaction Diagram
Cross-References
Annotations
Reactions
Reactions | Name | Structure | Kinetics | Depiction |
---|---|---|---|---|
ErkErk_act | Erk_Activation | cell | GeneralKinetics | |
Erk_actErk | Erk_Deactivation | cell | GeneralKinetics |
Erk_Activation Universal ID's
Erk_Activation Text Annotations
Erk_Deactivation Universal ID's
Erk_Deactivation Text Annotations
Expressions for Erk_Activation
reaction rate
J
(Kcat_act * Mek_act * Erk / (km_act + Erk)) [mmol.ml-1.min-1]
global
km_act
1007340.0 [mmol.ml-1]
global
Kcat_act
9.85367 [min-1]
Expressions for Erk_Deactivation
reaction rate
J
(Kcat_inact * PP2A_act * Erk_act / (km_inact + Erk_act)) [mmol.ml-1.min-1]
global
km_inact
3496490.0 [mmol.ml-1]
global
Kcat_inact
8.8912 [min-1]
Species
Name | Structure | BioNetGen Definition | Depiction |
---|---|---|---|
Mek_act | cell | MEK(Active~yes!-,). | |
Erk_act | cell | ERK(Phosphorylated~yes!-,). | |
Erk | cell | ERK(Phosphorylated~no!-,). | |
PP2A_act | cell | PP2A(Active~yes!-,). |
Mek_act Universal ID's
Mek_act Text Annotations
Erk_act Universal ID's
Erk_act Text Annotations
Erk Universal ID's
Erk Text Annotations
PP2A_act Universal ID's
PP2A_act Text Annotations
Molecules
Name | BioNetGen Definition | DEPICTION |
---|---|---|
MEK | MEK(Active~yes~no,) | |
ERK | ERK(Phosphorylated~yes~no,) | |
PP2A | PP2A(Active~yes~no,) |
MEK Universal ID's
MEK Text Annotations
ERK Universal ID's
ERK 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 PraneetDangol cloned from 'Deterministic' owned by user ModelBrick 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
Specifications (Reaction) - Deterministic go to Simulations
Simulations - Deterministic go to Specifications
Assignments
Name | Variable | Assignment Function Expression |
---|
Events
Name | Trigger Type | Variable Assignment |
---|
Geometry Compartmental968719063
(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 |
---|
Global Parameters
Name | Expression |
---|---|
km_inact | 3496490.0[mmol.ml-1] |
Kcat_inact | 8.8912[min-1] |
km_act | 1007340.0[mmol.ml-1] |
Kcat_act | 9.85367[min-1] |
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 |