Physiology

Reaction Diagram

reactionDiagram

Cross-References

Annotations

Reactions

Reactions
Name
Structure
Kinetics
Depiction
EGFR+EGFLR EGF_Binding_Unbinding compartment GeneralKinetics
LREGFR_deg EGFReceptor_Degradation compartment GeneralKinetics
proEGFREGFR EGFReceptor_Production compartment GeneralKinetics
EGFREGFR_deg EGFReceptor_Degradation_Free compartment GeneralKinetics

EGF_Binding_Unbinding Universal ID's

EGF_Binding_Unbinding Text Annotations

EGFReceptor_Degradation Universal ID's

EGFReceptor_Degradation Text Annotations

EGFReceptor_Production Universal ID's

EGFReceptor_Production Text Annotations

EGFReceptor_Degradation_Free Universal ID's

EGFReceptor_Degradation_Free Text Annotations

Expressions for EGF_Binding_Unbinding

reaction rate

J

((k1_EGFR * EGF * EGFR) - (k2_EGFR * LR)) [mmol.ml-1.min-1]

global

k1_EGFR

2.18503E-5 [ml.min-1.mmol-1]

global

k2_EGFR

0.121008 [min-1]

Expressions for EGFReceptor_Degradation

reaction rate

J

(k1_deg * LR) [mmol.ml-1.min-1]

global

k1_deg

0.2 [min-1]

Expressions for EGFReceptor_Production

reaction rate

J

v_EGFR [mmol.ml-1.min-1]

global

v_EGFR

100.0 [mmol.min-1.ml-1]

Expressions for EGFReceptor_Degradation_Free

reaction rate

J

(k1_deg * EGFR) [mmol.ml-1.min-1]

global

k1_deg

0.2 [min-1]

Structures

Name
Type
Electrical
compartment Compartment (+)   (-)

compartment Universal ID's

compartment Text Annotations

Species

Name
Structure
BioNetGen Definition
Depiction
LR compartment EGFR(Y~U!1,State~active!-,).EGF(Site0!1,). compartment
EGFR compartment EGFR(Y~U!-,State~active!-,). compartment
EGFR_deg compartment EGFR(Y~U!-,State~deg!-,). compartment
EGF compartment EGF(Site0!-,). compartment
proEGFR compartment EGFR(Y~U!-,State~deg!-,). compartment

LR Universal ID's

LR Text Annotations

EGFR Universal ID's

EGFR Text Annotations

EGFR_deg Universal ID's

EGFR_deg Text Annotations

EGF Universal ID's

EGF Text Annotations

proEGFR Universal ID's

proEGFR Text Annotations

Molecules

Name
BioNetGen Definition
DEPICTION
EGFR EGFR(Y~P~U,State~deg~active,)
EGF EGF(Site0,)
SOS SOS(Active~yes~no,)
Ras Ras(Active~yes~no,)
Raf Raf(Active~yes~no,)
MEK MEK(Active~yes~no,)
ERK ERK(Active~yes~no,)
P90Rsk P90Rsk(Active~yes~no,)
PI3K PI3K(Active~yes~no,)
Akt Akt(Active~yes~no,)
C3G C3G(Active~yes~no,)
Rap1 Rap1(Active~yes~no,)
B_Raf B_Raf(Active~yes~no,)
PP2A PP2A(Active~yes~no,)
P_tase P_tase()
GAP GAP()

EGFR Universal ID's

EGFR Text Annotations

EGF Universal ID's

EGF Text Annotations

SOS Universal ID's

SOS Text Annotations

Ras Universal ID's

Ras Text Annotations

Raf Universal ID's

Raf Text Annotations

MEK Universal ID's

MEK Text Annotations

ERK Universal ID's

ERK Text Annotations

P90Rsk Universal ID's

P90Rsk Text Annotations

PI3K Universal ID's

PI3K Text Annotations

Akt Universal ID's

Akt Text Annotations

C3G Universal ID's

C3G Text Annotations

Rap1 Universal ID's

Rap1 Text Annotations

B_Raf Universal ID's

B_Raf Text Annotations

PP2A Universal ID's

PP2A Text Annotations

P_tase Universal ID's

P_tase Text Annotations

GAP Universal ID's

GAP 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 mblinov 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] compartment
EGFR 80000.0 [mmol] 0.0 [m2/min] compartment
EGFR_deg 0.0 [mmol] 0.0 [m2/min] compartment
EGF 1.0002E7 [mmol] 0.0 [m2/min] compartment
proEGFR 1.0 [mmol] 0.0 [m2/min] compartment

Specifications (Reaction) - Deterministic go to Simulations

Name
Enabled?
EGF_Binding_Unbinding included
EGFReceptor_Degradation included
EGFReceptor_Production included
EGFReceptor_Degradation_Free included

Simulations - Deterministic go to Specifications

Name
End Time
Output Options
test 60.0

KeepEvery 1

KeepAtMost 1000

Deterministic Universal ID's

Deterministic Text Annotations

Assignments

Name Variable Assignment Function Expression

Events

Name Trigger Type Variable Assignment

Geometry Compartmental1940725914

(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 compartment

Events

Name Variable Rate Expression

Global Parameters

Name
Expression
k1_deg 0.2[min-1]
v_EGFR 100.0[mmol.min-1.ml-1]
k1_EGFR 2.18503E-5[ml.min-1.mmol-1]
k2_EGFR 0.121008[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