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Name - Rab5_switch

BioModel ID - 188458250

Reaction Diagram

reactionDiagram

Physiology

Universal ID's	Text Annotations

Reactions See in Dashboard
Reaction	Name Structure	Kinetics	Depiction
Rab5_GDP	Recruitment of Rab5_GDP endosome	GeneralLumpedKinetics	Rab5_GDP
		lumped reaction rate (LumpedJ): (endosome * K1)[mole.s-1] user defined (K1): 1.0[mol.s-1.l-1]
Rab5_GDPRab5_GTP	Activation of Rab5 endosome	GeneralLumpedKinetics	Rab5_GDPRab5_GTP
		lumped reaction rate (LumpedJ): (endosome * ((Rab5_GDP * ((ke * t) / (100.0 + t))) / (1.0 + exp(((kg - Rab5_GTP) * kf)))))[mole.s-1] user defined (ke): 0.3[s-1] user defined (kf): 2.5[M-1] user defined (kg): 0.1[M]
Rab5_GDP	extraction of Rab5_GDP endosome	GeneralLumpedKinetics	Rab5_GDP
		lumped reaction rate (LumpedJ): (endosome * (kminus1 * Rab5_GDP))[mole.s-1] user defined (kminus1): 1.0[s-1]
Rab5_GTPRab5_GDP	Hydrolysis of Rab5_GTP endosome	GeneralLumpedKinetics	Rab5_GTPRab5_GDP
		lumped reaction rate (LumpedJ): (endosome * ((ke * Rab5_GTP) / (1.0 + exp(((kg - Rab7_GTP) * kf)))))[mole.s-1] user defined (ke): 0.31[s-1] user defined (kf): 3.0[M-1] user defined (kg): 0.3[M]
Rab5_GTPRab5_GDP	Hydrolysis of Rab5_GTP_d endosome	GeneralLumpedKinetics	Rab5_GTPRab5_GDP
		lumped reaction rate (LumpedJ): (endosome * (kh * Rab5_GTP))[mole.s-1] user defined (kh): 0.06[s-1]

Structures See in Dashboard
Name	Type Electrical (Membrane Polarity)
endosome	Compartment (+) (-)

Species See in Dashboard
Name	Structure	BioNetGen Definition
Rab5_GDP	endosome	Rab5(BS!1,).GDP(BS!1,).

Rab5_GTP	endosome	Rab5(BS!1,).GTP(BS!1,).

Rab7_GTP	endosome	Rab7(BS!1,).GTP(BS!1,).

Molecules See in Dashboard
Name	Text Annotations	BioNetGen Definition
Rab5	Text Annotations	Rab5(BS,)

Rab7	Text Annotations	Rab7(BS,)

GTP	Text Annotations	GTP(BS,)

GDP	Text Annotations	GDP(BS,)

Observables See in Dashboard
Name	Type Count	BioNetGen Definition
O0_Rab5_tot	Molecules Multimolecular	Rab5(BS!?,).

O0_GTP_tot	Molecules Multimolecular	GTP(BS!?,).

O0_GDP_tot	Molecules Multimolecular	GDP(BS!?,).

Applications

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

Application - Deterministic

Specifications(Species) - Deterministic See in Dashboard
Species	Initial Condition	Diffusion Constant
Rab5_GDP	1.0 [mole]	0.0 [m2/s]
Rab5_GTP	0.001 [mole]	0.0 [m2/s]
Rab7_GTP	0.001 [mole]	0.0 [m2/s]

Specifications(Reaction) - Deterministic See in Dashboard
Name	Reaction Mapping
Recruitment of Rab5_GDP	included
Activation of Rab5	included
extraction of Rab5_GDP	included
Hydrolysis of Rab5_GTP	included
Hydrolysis of Rab5_GTP_d	included

Simulations - Deterministic See in Dashboard
Name	End Time	Output Options
Simulation0	1000.0 [s]	KeepEvery 1 KeepAtMost 1000

Geometry Compartmental1388779149 See in Dashboard
(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			endosome

Global Parameters

Global Parameters See in Dashboard
Name	Expression