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Name - Negative_feedback_oscillator

BioModel ID - 211728382

Reaction Diagram

reactionDiagram

Physiology

Universal ID's	Text Annotations

Reactions See in Dashboard
Reaction	Name Structure	Kinetics	Depiction
X	X_synthesis env	GeneralKinetics	X
		reaction rate (J): (k0 + (k1 * S))[mol.litre-1.s-1]
X	X_degradation env	GeneralKinetics	X
		reaction rate (J): ((k2 + (k2_prime * Rp)) * X)[mol.litre-1.s-1]
YYp	Y_phosphorylation env	GeneralKinetics	YYp
		reaction rate (J): (k3 * X * (Yt - Yp) / (Km3 + Yt - Yp))[mol.litre-1.s-1]
YpY	Y_dephosphorylation env	GeneralKinetics	YpY
		reaction rate (J): (k4 * Yp / (Km4 + Yp))[mol.litre-1.s-1]
RRp	R_phosphorylation env	GeneralKinetics	RRp
		reaction rate (J): (k5 * Yp * (Rt - Rp) / (Km5 + Rt - Rp))[mol.litre-1.s-1]
RpR	R_dephosphorylation env	GeneralKinetics	RpR
		reaction rate (J): (k6 * Rp / (Km6 + Rp))[mol.litre-1.s-1]

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

Species See in Dashboard
Name	Structure	BioNetGen Definition
Rp	env	R(mod~P!-,).

X	env	X().

Yp	env	Y(mod~P!-,).

S	env	S().

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

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

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

X	Text Annotations	X()

Y	Text Annotations	Y(mod~P~U,)

S	Text Annotations	S()

Observables See in Dashboard
Name	Type Count	BioNetGen Definition
O0_R_tot	Molecules Multimolecular	R(mod!?,).

O0_X_tot	Molecules Multimolecular	X().

O0_Y_tot	Molecules Multimolecular	Y(mod!?,).

O0_S_tot	Molecules Multimolecular	S().

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
Rp	0.0 [mol]	0.0 [m2/s]
X	0.0 [mol]	0.0 [m2/s]
Yp	0.0 [mol]	0.0 [m2/s]
S	0.0 [mol]	0.0 [m2/s]
Y	(Yt - Yp) [mol]	0.0 [m2/s]
R	(Rt - Rp) [mol]	0.0 [m2/s]

Specifications(Reaction) - Deterministic See in Dashboard
Name	Reaction Mapping
X_synthesis	included
X_degradation	included
Y_phosphorylation	included
Y_dephosphorylation	included
R_phosphorylation	included
R_dephosphorylation	included

Simulations - Deterministic See in Dashboard
Name	End Time	Output Options
Simulation0	1.0 [s]	KeepEvery 1 KeepAtMost 1000

Assignment Rules - Deterministic See in Dashboard
Name	Variable	Assignment Function Expression
assignmentRule0	R	(Rt - Rp)
assignmentRule1	Y	(Yt - Yp)

Geometry Compartmental2140009053 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	0.0[mol.s-1.l-1]

k1	1.0[s-1]

k2	0.01[s-1]

k2_prime	10.0[M-1.s-1]

k3	0.1[s-1]

Yt	1.0[M]

Km3	0.01[M]

k4	0.2[mol.s-1.l-1]

Km4	0.01[M]

k5	0.1[s-1]

Rt	1.0[M]

Km5	0.01[M]

k6	0.05[mol.s-1.l-1]

Km6	0.01[M]