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Name - Activator_inhibitor

BioModel ID - 188152002

Reaction Diagram

reactionDiagram

Physiology

Universal ID's	Text Annotations

Reactions See in Dashboard
Reaction	Name Structure	Kinetics	Depiction
R	R_synthesis env	GeneralKinetics	R
		reaction rate (J): (k0 * Ep)[mol.litre-1.s-1]
R	R_synthesis2 env	GeneralKinetics	R
		reaction rate (J): (k1 * S)[mol.litre-1.s-1]
R	R_degradation env	GeneralKinetics	R
		reaction rate (J): (k2 * R)[mol.litre-1.s-1]
R	R_degradation_by_X env	GeneralKinetics	R
		reaction rate (J): (k2_prime * R * X)[mol.litre-1.s-1]
EEp	E_phosphorylation env	GeneralKinetics	EEp
		reaction rate (J): (k3 * R * E / (Km3 + E))[mol.litre-1.s-1]
EpE	E_dephosphorylation env	GeneralKinetics	EpE
		reaction rate (J): (k4 * Ep / (Km4 + Ep))[mol.litre-1.s-1]
X	X_synthesis env	GeneralKinetics	X
		reaction rate (J): (k5 * R)[mol.litre-1.s-1]
X	X_degradation env	GeneralKinetics	X
		reaction rate (J): (k6 * X)[mol.litre-1.s-1]

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

Species See in Dashboard
Name	Structure	BioNetGen Definition
R	env	R().

X	env	X().

S	env	S().

E	env	E(mod~U!-,).

Ep	env	E(mod~P!-,).

Molecules See in Dashboard
Name	Text Annotations	BioNetGen Definition
E	Text Annotations	E(mod~P~U,)

S	Text Annotations	S()

R	Text Annotations	R()

X	Text Annotations	X()

Observables See in Dashboard
Name	Type Count	BioNetGen Definition
O0_E_tot	Molecules Multimolecular	E(mod!?,).

O0_S_tot	Molecules Multimolecular	S().

O0_R_tot	Molecules Multimolecular	R().

O0_X_tot	Molecules Multimolecular	X().

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
R	0.0 [mol]	0.0 [m2/s]
X	0.0 [mol]	0.0 [m2/s]
S	0.0 [mol]	0.0 [m2/s]
E	(Et - Ep) [mol]	0.0 [m2/s]
Ep	(((2.0 * (k3 * R) * J4) / ((k4 - (k3 * R)) + (J3 * k4) + (J4 * (k3 * R)) + pow((pow(((k4 - (k3 * R)) + (J3 * k4) + (J4 * (k3 * R))),2.0) - (4.0 * (k4 - (k3 * R)) * (k3 * R) * J4)),(1.0 / 2.0)))) * Et) [mol]	0.0 [m2/s]

Specifications(Reaction) - Deterministic See in Dashboard
Name	Reaction Mapping
R_synthesis	included
R_synthesis2	included
R_degradation	included
R_degradation_by_X	included
E_phosphorylation	included
E_dephosphorylation	included
X_synthesis	included
X_degradation	included

Simulations - Deterministic See in Dashboard
Name	End Time	Output Options
Simulation0	10.0 [s]	KeepEvery 1 KeepAtMost 1000

Assignment Rules - Deterministic See in Dashboard
Name	Variable	Assignment Function Expression
assignmentRule0	Km3	(J3 * Et)
assignmentRule1	Km4	(J4 * Et)
assignmentRule2	E	(Et - Ep)
assignmentRule3	Ep	(((2.0 * (k3 * R) * J4) / ((k4 - (k3 * R)) + (J3 * k4) + (J4 * (k3 * R)) + pow((pow(((k4 - (k3 * R)) + (J3 * k4) + (J4 * (k3 * R))),2.0) - (4.0 * (k4 - (k3 * R)) * (k3 * R) * J4)),(1.0 / 2.0)))) * Et)

Geometry Compartmental 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			env

Global Parameters

Global Parameters See in Dashboard
Name	Expression
k0	4.0[s-1]

k1	1.0[s-1]

k2	1.0[s-1]

k2_prime	1.0[M-1.s-1]

k3	1.0[s-1]

J3	0.3[1]

k4	1.0[mol.s-1.l-1]

J4	0.3[1]

k5	0.1[s-1]

k6	0.075[s-1]

Et	1.0[M]

Km3	(J3 * Et)[M]

Km4	(J4 * Et)[M]