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

Structures

Name
Type
Electrical
cell Compartment (+)   (-)

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

Molecules

Name
BioNetGen Definition
DEPICTION
MEK MEK(Active~yes~no,)
ERK ERK(Phosphorylated~yes~no,)
PP2A PP2A(Active~yes~no,)

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

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]

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