Physiology

Reaction Diagram

reactionDiagram

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]

Structures

Name
Type
Electrical
cell Compartment (+)   (-)

cell Universal ID's

cell Text Annotations

Species

Name
Structure
BioNetGen Definition
Depiction
Mek_act cell MEK(Active~yes!-,). cell
Erk_act cell ERK(Phosphorylated~yes!-,). cell
Erk cell ERK(Phosphorylated~no!-,). cell
PP2A_act cell PP2A(Active~yes!-,). cell

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

Observables

Name
Structure
Count
BNGL Definition
Sequence Type
DEPICTION

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

Species
Initial Condition
Diffusion Constant
Structure
Mek_act 0.0 [mmol] 0.0 [m2/min] cell
Erk_act 0.0 [mmol] 0.0 [m2/min] cell
Erk 600000.0 [mmol] 0.0 [m2/min] cell
PP2A_act 120000.0 [mmol] 0.0 [m2/min] cell

Specifications (Reaction) - Deterministic go to Simulations

Name
Enabled?
Erk_Activation included
Erk_Deactivation included

Simulations - Deterministic go to Specifications

Name
End Time
Output Options

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