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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
-->Rab5_GDP	Recruitment of Rab5_GDP endosome	GeneralLumpedKinetics
Universal ID's:	Text Annotations:	lumped reaction rate (LumpedJ): (endosome * K1)[mole.s-1] user defined (K1): 1.0[mol.s-1.l-1]
Rab5_GDP-->Rab5_GTP	Activation of Rab5 endosome	GeneralLumpedKinetics
Universal ID's:	Text Annotations:	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
Universal ID's:	Text Annotations:	lumped reaction rate (LumpedJ): (endosome * (kminus1 * Rab5_GDP))[mole.s-1] user defined (kminus1): 1.0[s-1]
Rab5_GTP-->Rab5_GDP	Hydrolysis of Rab5_GTP endosome	GeneralLumpedKinetics
Universal ID's:	Text Annotations:	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_GTP-->Rab5_GDP	Hydrolysis of Rab5_GTP_d endosome	GeneralLumpedKinetics
Universal ID's:	Text Annotations:	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 (+) (-)
Universal ID's:	Text Annotations:

Species See in Dashboard
Name	Structure	BioNetGen Definition
Rab5_GDP	endosome	Rab5(BS!1,).GDP(BS!1,).
Universal ID's:	Text Annotations:
Rab5_GTP	endosome	Rab5(BS!1,).GTP(BS!1,).
Universal ID's:	Text Annotations:
Rab7_GTP	endosome	Rab7(BS!1,).GTP(BS!1,).
Universal ID's:	Text Annotations:

Molecules See in Dashboard
Name	Text Annotations	BioNetGen Definition
Rab5	Text Annotations	Rab5(BS,)
Universal ID's:
Rab7	Text Annotations	Rab7(BS,)
Universal ID's:
GTP	Text Annotations	GTP(BS,)
Universal ID's:
GDP	Text Annotations	GDP(BS,)
Universal ID's:

Observables See in Dashboard
Name	Type Count	BioNetGen Definition
O0_Rab5_tot	Molecules Multimolecular	Rab5(BS!?,).
Universal ID's:	Text Annotations:
O0_GTP_tot	Molecules Multimolecular	GTP(BS!?,).
Universal ID's:	Text Annotations:
O0_GDP_tot	Molecules Multimolecular	GDP(BS!?,).
Universal ID's:	Text Annotations:

Applications

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

0 - Deterministic

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

Global Parameters

Global Parameters See in Dashboard
Name	Expression