Physiology

Reaction Diagram

reactionDiagram

Cross-References

Annotations

Reactions

Reactions
Name
Structure
Kinetics
Depiction
PI3KPI3K_act PI3K_Activation_EGFR cell GeneralKinetics
PI3KPI3K_act PI3K_Activation_Ras cell GeneralKinetics
PI3K_actPI3K PI3K_Deactivation cell GeneralKinetics

PI3K_Activation_EGFR Universal ID's

PI3K_Activation_EGFR Text Annotations

PI3K_Activation_Ras Universal ID's

PI3K_Activation_Ras Text Annotations

PI3K_Deactivation Universal ID's

PI3K_Deactivation Text Annotations

Expressions for PI3K_Activation_EGFR

reaction rate

J

(Kcat_act * LR * PI3K / (km_act + PI3K)) [mmol.ml-1.min-1]

global

Kcat_act

10.6737 [min-1]

global

km_act

184912.0 [mmol.ml-1]

Expressions for PI3K_Activation_Ras

reaction rate

J

(Kcat_PI3Kact * Ras_act * PI3K / (km_PI3K_act + PI3K)) [mmol.ml-1.min-1]

global

km_PI3K_act

272056.0 [mmol.ml-1]

global

Kcat_PI3Kact

0.0771067 [min-1]

Expressions for PI3K_Deactivation

reaction rate

J

(k1_act * PI3K_act) [mmol.ml-1.min-1]

global

k1_act

0.005 [min-1]

Structures

Name
Type
Electrical
cell Compartment (+)   (-)

cell Universal ID's

cell Text Annotations

Species

Name
Structure
BioNetGen Definition
Depiction
LR cell EGF(EGF!1,).EGFR(ecd!1,Y~P!-,). cell
Ras_act cell Ras(Active~yes!-,). cell
PI3K_act cell PI3K(Active~yes!-,). cell
PI3K cell PI3K(Active~no!-,). cell

LR Universal ID's

LR Text Annotations

Ras_act Universal ID's

Ras_act Text Annotations

PI3K_act Universal ID's

PI3K_act Text Annotations

PI3K Universal ID's

PI3K Text Annotations

Molecules

Name
BioNetGen Definition
DEPICTION
EGFR EGFR(ecd,Y~P~U,)
EGF EGF(EGF,)
Ras Ras(Active~yes~no,)
PI3K PI3K(Active~yes~no,)

EGFR Universal ID's

EGFR Text Annotations

EGF Universal ID's

EGF Text Annotations

Ras Universal ID's

Ras Text Annotations

PI3K Universal ID's

PI3K 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
LR 0.0 [mmol] 0.0 [m2/min] cell
Ras_act 0.0 [mmol] 0.0 [m2/min] cell
PI3K_act 0.0 [mmol] 0.0 [m2/min] cell
PI3K 120000.0 [mmol] 0.0 [m2/min] cell

Specifications (Reaction) - Deterministic go to Simulations

Name
Enabled?
PI3K_Activation_EGFR included
PI3K_Activation_Ras included
PI3K_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 Compartmental1573685769

(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
Kcat_act 10.6737[min-1]
km_act 184912.0[mmol.ml-1]
km_PI3K_act 272056.0[mmol.ml-1]
Kcat_PI3Kact 0.0771067[min-1]
k1_act 0.005[min-1]

Universal ID's

Text Annotations

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