Physiology

Reaction Diagram

reactionDiagram

Cross-References

Annotations

Reactions

Reactions
Name
Structure
Kinetics
Depiction
pYA+SH2ApYASH2A r4 membrane MassAction
YA+Kinase_EGFpYA+Kinase_EGF r7 membrane MassAction
kinase+EGFKinase_EGF r6 membrane MassAction
pYAYA r0 membrane HMMIrreversible
pYA+SH2BpYASH2B r1 membrane MassAction

r4 Universal ID's

r4 Text Annotations

r7 Universal ID's

r7 Text Annotations

r6 Universal ID's

r6 Text Annotations

r0 Universal ID's

r0 Text Annotations

r1 Universal ID's

r1 Text Annotations

Expressions for r4

reaction rate

J

(((Kf * pYA) * SH2A) - (Kr * pYASH2A)) [uM.s-1]

forward rate constant

Kf

1.0 [s-1.uM-1]

reverse rate constant

Kr

1.5 [s-1]

Expressions for r7

reaction rate

J

(((Kf * YA) * Kinase_EGF) - ((Kr * pYA) * Kinase_EGF)) [uM.s-1]

forward rate constant

Kf

0.54 [s-1.uM-1]

reverse rate constant

Kr

0.0 [s-1.uM-1]

Expressions for r6

reaction rate

J

(((Kf * kinase) * EGF) - (Kr * Kinase_EGF)) [uM.s-1]

forward rate constant

Kf

63.0 [s-1.uM-1]

reverse rate constant

Kr

0.16 [s-1]

Expressions for r0

reaction rate

J

((Vmax * pYA) / (Km + pYA)) [uM.s-1]

Km (1/2 max)

Km

0.33 [uM]

max reaction rate

Vmax

0.93 [uM.s-1]

Expressions for r1

reaction rate

J

(((Kf * pYA) * SH2B) - (Kr * pYASH2B)) [uM.s-1]

forward rate constant

Kf

1.0 [s-1.uM-1]

reverse rate constant

Kr

1.5 [s-1]

Structures

Name
Type
Electrical
nuclear membrane Compartment (+)   (-)
cytoplasm Compartment (+)   (-)
extracellular Compartment (+)   (-)
membrane Compartment (+)   (-)
nucleus Compartment (+)   (-)

nuclear membrane Universal ID's

nuclear membrane Text Annotations

cytoplasm Universal ID's

cytoplasm Text Annotations

extracellular Universal ID's

extracellular Text Annotations

membrane Universal ID's

membrane Text Annotations

nucleus Universal ID's

nucleus Text Annotations

Species

Name
Structure
BioNetGen Definition
Depiction
SH2A cytoplasm cytoplasm
pYA membrane membrane
YA membrane membrane
pYASH2A membrane membrane
pYASH2B membrane membrane
SH2B cytoplasm cytoplasm
Kinase_EGF membrane membrane
kinase membrane membrane
EGF extracellular extracellular

SH2A Universal ID's

SH2A Text Annotations

pYA Universal ID's

pYA Text Annotations

YA Universal ID's

YA Text Annotations

pYASH2A Universal ID's

pYASH2A Text Annotations

pYASH2B Universal ID's

pYASH2B Text Annotations

SH2B Universal ID's

SH2B Text Annotations

Kinase_EGF Universal ID's

Kinase_EGF Text Annotations

kinase Universal ID's

kinase Text Annotations

EGF Universal ID's

EGF Text Annotations

Molecules

Name
BioNetGen Definition
DEPICTION

Observables

Name
Structure
Count
BNGL Definition
Sequence Type
DEPICTION

Applications

Name
Properties Math Type
Annotation
Application2 Specs - Species
Specs - Reaction
Simulations 		Deterministic (ODE) Compartmental

Application2 Universal ID's

Application2 Text Annotations

Specifications (Species) - Application2 go to Simulations

Species
Initial Condition
Diffusion Constant
Structure
SH2A 0.24 [uM] 0.0 [um2/s] cytoplasm
SH2B 0.0 [uM] 0.0 [um2/s] cytoplasm
EGF 4.0E-4 [uM] 0.0 [um2/s] extracellular
pYA 0.0 [uM] 0.0 [um2/s] membrane
YA 8.1 [uM] 0.0 [um2/s] membrane
pYASH2A 0.0 [uM] 0.0 [um2/s] membrane
pYASH2B 0.0 [uM] 0.0 [um2/s] membrane
Kinase_EGF 0.0 [uM] 0.0 [um2/s] membrane
kinase 0.81 [uM] 0.0 [um2/s] membrane

Specifications (Reaction) - Application2 go to Simulations

Name
Enabled?
r4 included
r7 included
r6 included
r0 included
r1 included

Simulations - Application2 go to Specifications

Name
End Time
Output Options
Simulation1 100.0

OutputTimeStep 5.0
Copy of Simulation1 100.0

OutputTimeStep 5.0
Simulation0 100.0

OutputTimeStep 5.0
Simulation2 1000.0

OutputTimeStep 5.0
Simulation3 1000.0

OutputTimeStep 5.0
Copy of Simulation3 1000.0

OutputTimeStep 5.0

Application2 Universal ID's

Application2 Text Annotations

Application2 Universal ID's

Application2 Text Annotations

Application2 Universal ID's

Application2 Text Annotations

Application2 Universal ID's

Application2 Text Annotations

Application2 Universal ID's

Application2 Text Annotations

Application2 Universal ID's

Application2 Text Annotations

Assignments

Name Variable Assignment Function Expression

Events

Name Trigger Type Variable Assignment

Geometry non-spatial210953455

(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 nucleus

Events

Name Variable Rate Expression

Global Parameters

Name
Expression

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 Application2.bngl
SBML Application2.sbml
Matlab Application2.m
NFSim XML Application2.xml