ModelBricks - Model Print Page

Dashboard

Name - Cell_Ca_oscillation

BioModel ID - 222213505

Reaction Diagram

reactionDiagram

Physiology

Universal ID's	Text Annotations

Reactions See in Dashboard
Reaction	Name Structure	Kinetics	Depiction
Ca_cell1	IP3R mediated Ca release Cell1 Cytosol	GeneralLumpedKinetics	Ca_cell1
		lumped reaction rate (LumpedJ): (Cytosol * kf * pow(((p * IP3R_cell1 * Phi1_c1) / ((Phi1_c1 * p) + Phi_minus1_c1)),4.0))[umol.s-1] user defined (p): 0.2778[tbd] user defined (kf): 28.0[tbd]
Ca_cell1	ATPase pump mediated Ca release Cell1 Cytosol	GeneralLumpedKinetics	Ca_cell1
		lumped reaction rate (LumpedJ): (Cytosol * ((Vp * pow(Ca_cell1,2.0)) / (pow(Kp,2.0) + pow(Ca_cell1,2.0))))[umol.s-1] user defined (Kp): 0.18[tbd] user defined (Vp): 1.2[tbd]
Ca_cell1	IP3R independent Ca release Cell1 Cytosol	GeneralLumpedKinetics	Ca_cell1
		lumped reaction rate (LumpedJ): (Cytosol * Jleak)[umol.s-1] user defined (Jleak): 0.2[umol.s-1.litre-1]
IP3R_cell1	IP3R Inactive to Shut transtition cell1 Cytosol	GeneralLumpedKinetics	IP3R_cell1
		lumped reaction rate (LumpedJ): (Cytosol * Phi3_c1 * (1.0 - IP3R_cell1))[umol.s-1]
IP3R_cell1	IP3R Open_to_Inactivated_Cell1 Cytosol	GeneralLumpedKinetics	IP3R_cell1
		lumped reaction rate (LumpedJ): ((Cytosol * Phi1_c1 * Phi2_c1 * IP3R_cell1 * p) / ((Phi1_c1 * p) + Phi_minus1_c1))[umol.s-1] user defined (p): 0.2778[tbd]

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

Species See in Dashboard
Name	Structure	BioNetGen Definition
Ca_cell1	Cytosol	Ca().

IP3R_cell1	Cytosol	IP3R_cell1(Ca_bs!-,).

Molecules See in Dashboard
Name	Text Annotations	BioNetGen Definition
Ca	Text Annotations	Ca()

IP3R_cell1	Text Annotations	IP3R_cell1(Ca_bs,)

Observables See in Dashboard
Name	Type Count	BioNetGen Definition
O0_Ca_tot	Molecules Multimolecular	Ca().

O0_IP3R_cell1_tot	Molecules Multimolecular	IP3R_cell1(Ca_bs!?,).

Applications

Applications See in Dashboard
Name	Math Type	Annotation
Deterministic 1	Deterministic (ODE) Compartmental
Deterministic 2	Deterministic (ODE) Compartmental	(copied from Deterministic 1)

Application - Deterministic 1

Specifications(Species) - Deterministic 1 See in Dashboard
Species	Initial Condition	Diffusion Constant
Ca_cell1	0.3 [umol]	0.0 [m2/s]
IP3R_cell1	0.8 [umol]	0.0 [m2/s]

Specifications(Reaction) - Deterministic 1 See in Dashboard
Name	Reaction Mapping
IP3R mediated Ca release Cell1	included
ATPase pump mediated Ca release Cell1	included
IP3R independent Ca release Cell1	included
IP3R Inactive to Shut transtition cell1	included
IP3R Open_to_Inactivated_Cell1	included

Simulations - Deterministic 1 See in Dashboard
Name	End Time	Output Options
Simulation1	30.0 [s]	KeepEvery 1 KeepAtMost 1000

Geometry Compartmental2132244465 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			Cytosol

Application - Deterministic 2

Specifications(Species) - Deterministic 2 See in Dashboard
Species	Initial Condition	Diffusion Constant
Ca_cell1	0.3 [umol]	0.0 [m2/s]
IP3R_cell1	0.8 [umol]	0.0 [m2/s]

Specifications(Reaction) - Deterministic 2 See in Dashboard
Name	Reaction Mapping
IP3R mediated Ca release Cell1	included
ATPase pump mediated Ca release Cell1	included
IP3R independent Ca release Cell1	included
IP3R Inactive to Shut transtition cell1	included
IP3R Open_to_Inactivated_Cell1	included

Simulations - Deterministic 2 See in Dashboard
Name	End Time	Output Options
Simulation1_1	30.0 [s]	KeepEvery 1 KeepAtMost 1000

Geometry Compartmental1280423882 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			Cytosol

Global Parameters

Global Parameters See in Dashboard
Name	Expression
Phi1_c1	((r2 * Ca_cell1) / (R1 + Ca_cell1))[tbd]

r2	100.0[tbd]

R1	6.0[tbd]

Phi_minus1_c1	(k1 / (R3 + Ca_cell1))[tbd]

k1	44.0[tbd]

R3	50.0[tbd]

Phi2_c1	((k2 + (r4 * Ca_cell1)) / (R3 + Ca_cell1))[tbd]

k2	26.5[tbd]

r4	20.0[tbd]

Phi3_c1	(k3 / (R5 + Ca_cell1))[tbd]

k3	1.6[tbd]

R5	1.6[tbd]