Physiology

Reaction Diagram

reactionDiagram

Cross-References

Annotations

Reactions

Reactions
Name
Structure
Kinetics
Erk Erk_act Erk_Activation cell GeneralKinetics
Erk_act Erk 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]

Expressions for Erk_Deactivation

reaction rate

J

(Kcat_inact * PP2A_act * Erk_act / (km_inact + Erk_act)) [mmol.ml-1.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!-,).
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

Observables

Name
Structure
Count
BNGL Definition
Sequence Type
DEPICTION

Applications

Name
Properties Math Type
Deterministic Specs - Species
Specs - Reaction
Simulations 		Deterministic (ODE) Compartmental

Deterministic Text Annotations

Deterministic Universal ID's

Annotations will come here

RFID | pubmed

Specifications (Species) - Deterministic go to Simulations

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

Specifications (Reaction) - Deterministic go to Simulations

Name
Enabled?
Erk_Activation included
Erk_Deactivation included

Simulations - Deterministic go to Specifications

Name
End Time
Output Options

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

Format
File
VCML VCML File
BNGL
MatLab
SBML
Formatted XML
SEDML