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Name - spatial protection test- two way competition orginal - paper model shared

BioModel ID - 123269480

Reaction Diagram

reactionDiagram

Physiology

Universal ID's	Text Annotations

Reactions See in Dashboard
Reaction	Name Structure	Kinetics	Depiction
pYA+SH2ApYASH2A	r4 membrane	MassAction	pYA+SH2ApYASH2A
		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]
YA+Kinase_EGFpYA+Kinase_EGF	r7 membrane	MassAction	YA+Kinase_EGFpYA+Kinase_EGF
		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]
kinase+EGFKinase_EGF	r6 membrane	MassAction	kinase+EGFKinase_EGF
		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]
pYAYA	r0 membrane	HMMIrreversible	pYAYA
		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]
pYA+SH2BpYASH2B	r1 membrane	MassAction	pYA+SH2BpYASH2B
		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 See in Dashboard
Name	Type Electrical (Membrane Polarity)
nuclear membrane	Compartment (+) (-)

cytoplasm	Compartment (+) (-)

extracellular	Compartment (+) (-)

membrane	Compartment (+) (-)

nucleus	Compartment (+) (-)

Species See in Dashboard
Name	Structure	BioNetGen Definition
SH2A	cytoplasm

pYA	membrane

YA	membrane

pYASH2A	membrane

pYASH2B	membrane

SH2B	cytoplasm

Kinase_EGF	membrane

kinase	membrane

EGF	extracellular

Molecules See in Dashboard
Name	Text Annotations	BioNetGen Definition

Observables See in Dashboard
Name	Type Count	BioNetGen Definition

Applications

Applications See in Dashboard
Name	Math Type	Annotation
Application2	Deterministic (ODE) Compartmental

Application - Application2

Specifications(Species) - Application2 See in Dashboard
Species	Initial Condition	Diffusion Constant
SH2A	0.24 [uM]	0.0 [um2/s]
SH2B	0.0 [uM]	0.0 [um2/s]
EGF	4.0E-4 [uM]	0.0 [um2/s]
pYA	0.0 [uM]	0.0 [um2/s]
YA	8.1 [uM]	0.0 [um2/s]
pYASH2A	0.0 [uM]	0.0 [um2/s]
pYASH2B	0.0 [uM]	0.0 [um2/s]
Kinase_EGF	0.0 [uM]	0.0 [um2/s]
kinase	0.81 [uM]	0.0 [um2/s]

Specifications(Reaction) - Application2 See in Dashboard
Name	Reaction Mapping
r4	included
r7	included
r6	included
r0	included
r1	included

Simulations - Application2 See in Dashboard
Name	End Time	Output Options
Simulation1	100.0 [s]	OutputTimeStep 5.0
Copy of Simulation1	100.0 [s]	OutputTimeStep 5.0
Simulation0	100.0 [s]	OutputTimeStep 5.0
Simulation2	1000.0 [s]	OutputTimeStep 5.0
Simulation3	1000.0 [s]	OutputTimeStep 5.0
Copy of Simulation3	1000.0 [s]	OutputTimeStep 5.0

Geometry non-spatial210953455 See in Dashboard
(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

Global Parameters

Global Parameters See in Dashboard
Name	Expression