Physiology

Reaction Diagram

reactionDiagram

Cross-References

Annotations

Reactions

Reactions
Name
Structure
Kinetics
Depiction
pEGFR+SH2pEGFRSH2 r4 c0 GeneralKinetics
EGFRSH2EGFR+SH2 r5 c0 GeneralKinetics
pEGFRiEGFR r2 c0 GeneralKinetics
iEGFR r3 c0 GeneralKinetics
iEGFRSH2SH2 r8 c0 GeneralKinetics
iEGFR+SH2iEGFRSH2 r9 c0 GeneralKinetics
EGF+EGFRSH2pEGFRSH2 r6 c0 GeneralKinetics
pEGFRSH2iEGFRSH2 r7 c0 GeneralKinetics
EGFR r1 c0 GeneralKinetics
EGFR+EGFpEGFR r0 c0 GeneralKinetics

r4 Universal ID's

r4 Text Annotations

r5 Universal ID's

r5 Text Annotations

r2 Universal ID's

r2 Text Annotations

r3 Universal ID's

r3 Text Annotations

r8 Universal ID's

r8 Text Annotations

r9 Universal ID's

r9 Text Annotations

r6 Universal ID's

r6 Text Annotations

r7 Universal ID's

r7 Text Annotations

r1 Universal ID's

r1 Text Annotations

r0 Universal ID's

r0 Text Annotations

Expressions for r4

reaction rate

J

((kon * SH2 * pEGFR) - (koff * pEGFRSH2)) [uM.s-1]

global

kon

0.1 [s-1.uM-1]

global

koff

1.0 [s-1]

Expressions for r5

reaction rate

J

(koff * EGFRSH2) [uM.s-1]

global

koff

1.0 [s-1]

Expressions for r2

reaction rate

J

(ke * pEGFR) [uM.s-1]

local

ke

0.1 [s-1]

Expressions for r3

reaction rate

J

(kdeg * iEGFR) [uM.s-1]

global

kdeg

0.05 [s-1]

Expressions for r8

reaction rate

J

(kdeg * iEGFRSH2) [uM.s-1]

global

kdeg

0.05 [s-1]

Expressions for r9

reaction rate

J

((kon * SH2 * iEGFR) - (koff * iEGFRSH2)) [uM.s-1]

global

kon

0.1 [s-1.uM-1]

global

koff

1.0 [s-1]

Expressions for r6

reaction rate

J

((kf * EGF * EGFRSH2) - (kr * pEGFRSH2)) [uM.s-1]

global

kf

0.1 [s-1.uM-1]

global

kr

0.1 [s-1]

Expressions for r7

reaction rate

J

(keSH2 * pEGFRSH2) [uM.s-1]

local

keSH2

0.1 [s-1]

Expressions for r1

reaction rate

J

(Vsyn - (kt * EGFR)) [uM.s-1]

local

kt

0.01 [s-1]

local

Vsyn

1.0 [uM.s-1]

Expressions for r0

reaction rate

J

((kf * EGF * EGFR) - (kr * pEGFR)) [uM.s-1]

global

kf

0.1 [s-1.uM-1]

global

kr

0.1 [s-1]

Structures

Name
Type
Electrical
c0 Compartment (+)   (-)

c0 Universal ID's

c0 Text Annotations

Species

Name
Structure
BioNetGen Definition
Depiction
pEGFR c0 c0
iEGFR c0 c0
SH2 c0 c0
pEGFRSH2 c0 c0
EGFRSH2 c0 c0
iEGFRSH2 c0 c0
EGF c0 c0
EGFR c0 c0

pEGFR Universal ID's

pEGFR Text Annotations

iEGFR Universal ID's

iEGFR Text Annotations

SH2 Universal ID's

SH2 Text Annotations

pEGFRSH2 Universal ID's

pEGFRSH2 Text Annotations

EGFRSH2 Universal ID's

EGFRSH2 Text Annotations

iEGFRSH2 Universal ID's

iEGFRSH2 Text Annotations

EGF Universal ID's

EGF Text Annotations

EGFR Universal ID's

EGFR Text Annotations

Molecules

Name
BioNetGen Definition
DEPICTION

Observables

Name
Structure
Count
BNGL Definition
Sequence Type
DEPICTION

Applications

Name
Properties Math Type
Annotation
Application0 Specs - Species
Specs - Reaction
Simulations 		Deterministic (ODE) Compartmental

Application0 Universal ID's

Application0 Text Annotations

Specifications (Species) - Application0 go to Simulations

Species
Initial Condition
Diffusion Constant
Structure
pEGFR 0.0 [uM] 0.0 [um2/s] c0
iEGFR 0.0 [uM] 0.0 [um2/s] c0
SH2 0.0 [uM] 0.0 [um2/s] c0
pEGFRSH2 0.0 [uM] 0.0 [um2/s] c0
EGFRSH2 0.0 [uM] 0.0 [um2/s] c0
iEGFRSH2 0.0 [uM] 0.0 [um2/s] c0
EGF 1.0 [uM] 0.0 [um2/s] c0
EGFR 100.0 [uM] 0.0 [um2/s] c0

Specifications (Reaction) - Application0 go to Simulations

Name
Enabled?
r4 included
r5 included
r2 included
r3 included
r8 included
r9 included
r6 included
r7 included
r1 included
r0 included

Simulations - Application0 go to Specifications

Name
End Time
Output Options
Complex internalizes at turnover rate; vary koff and [SH2] 1 120.0

OutputTimeStep 1.0
Vary EGF, no SH2 120.0

OutputTimeStep 1.0

Application0 Universal ID's

Application0 Text Annotations

Application0 Universal ID's

Application0 Text Annotations

Assignments

Name Variable Assignment Function Expression

Events

Name Trigger Type Variable Assignment

Geometry non-spatial1211055930

(Origin: 0.0, 0.0, 0.0; Extent: 10.0, 10.0, 10.0 [um])

Dimension Type Subdomain Adjacent Subvolumes Size Mapped Compartment
Compartmental Compartment c0

Events

Name Variable Rate Expression

Global Parameters

Name
Expression
kf 0.1[s-1.uM-1]
kr 0.1[s-1]
kdeg 0.05[s-1]
kon 0.1[s-1.uM-1]
koff 1.0[s-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 Application0.bngl
SBML Application0.sbml
Matlab Application0.m
NFSim XML Application0.xml