Physiology

Reaction Diagram

reactionDiagram

Cross-References

Annotations

Reactions

Reactions
Name
Structure
Kinetics
Depiction
Ca_cell1 IP3R mediated Ca release Cell1 Cytosol GeneralLumpedKinetics
Ca_cell1 ATPase pump mediated Ca release Cell1 Cytosol GeneralLumpedKinetics
Ca_cell1 IP3R independent Ca release Cell1 Cytosol GeneralLumpedKinetics
IP3R_cell1 IP3R Inactive to Shut transtition cell1 Cytosol GeneralLumpedKinetics
IP3R_cell1 IP3R Open_to_Inactivated_Cell1 Cytosol GeneralLumpedKinetics

IP3R mediated Ca release Cell1 Universal ID's

IP3R mediated Ca release Cell1 Text Annotations

ATPase pump mediated Ca release Cell1 Universal ID's

ATPase pump mediated Ca release Cell1 Text Annotations

IP3R independent Ca release Cell1 Universal ID's

IP3R independent Ca release Cell1 Text Annotations

IP3R Inactive to Shut transtition cell1 Universal ID's

IP3R Inactive to Shut transtition cell1 Text Annotations

IP3R Open_to_Inactivated_Cell1 Universal ID's

IP3R Open_to_Inactivated_Cell1 Text Annotations

Expressions for IP3R mediated Ca release Cell1

lumped reaction rate

LumpedJ

(Cytosol * kf * pow(((p * IP3R_cell1 * Phi1_c1) / ((Phi1_c1 * p) + Phi_minus1_c1)),4.0)) [umol.s-1]

global

Phi1_c1

((r2 * Ca_cell1) / (R1 + Ca_cell1)) [tbd]

global

Phi_minus1_c1

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

local

p

0.2778 [tbd]

local

kf

28.0 [tbd]

Expressions for ATPase pump mediated Ca release Cell1

lumped reaction rate

LumpedJ

(Cytosol * ((Vp * pow(Ca_cell1,2.0)) / (pow(Kp,2.0) + pow(Ca_cell1,2.0)))) [umol.s-1]

local

Kp

0.18 [tbd]

local

Vp

1.2 [tbd]

Expressions for IP3R independent Ca release Cell1

lumped reaction rate

LumpedJ

(Cytosol * Jleak) [umol.s-1]

local

Jleak

0.2 [umol.s-1.litre-1]

Expressions for IP3R Inactive to Shut transtition cell1

lumped reaction rate

LumpedJ

(Cytosol * Phi3_c1 * (1.0 - IP3R_cell1)) [umol.s-1]

global

Phi3_c1

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

Expressions for IP3R Open_to_Inactivated_Cell1

lumped reaction rate

LumpedJ

((Cytosol * Phi1_c1 * Phi2_c1 * IP3R_cell1 * p) / ((Phi1_c1 * p) + Phi_minus1_c1)) [umol.s-1]

global

Phi1_c1

((r2 * Ca_cell1) / (R1 + Ca_cell1)) [tbd]

global

Phi_minus1_c1

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

global

Phi2_c1

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

local

p

0.2778 [tbd]

Structures

Name
Type
Electrical
Cytosol Compartment (+)   (-)

Cytosol Universal ID's

Cytosol Text Annotations

Species

Name
Structure
BioNetGen Definition
Depiction
Ca_cell1 Cytosol Ca(). Cytosol
IP3R_cell1 Cytosol IP3R_cell1(Ca_bs!-,). Cytosol

Ca_cell1 Universal ID's

Ca_cell1 Text Annotations

IP3R_cell1 Universal ID's

IP3R_cell1 Text Annotations

Molecules

Name
BioNetGen Definition
DEPICTION
Ca Ca()
IP3R_cell1 IP3R_cell1(Ca_bs,)

Ca Universal ID's

Ca Text Annotations

IP3R_cell1 Universal ID's

IP3R_cell1 Text Annotations

Observables

Name
Structure
Count
BNGL Definition
Sequence Type
DEPICTION
O0_Ca_tot Cytosol Molecules Ca(). Multimolecular
O0_IP3R_cell1_tot Cytosol Molecules IP3R_cell1(Ca_bs!?,). Multimolecular

O0_Ca_tot Universal ID's

O0_Ca_tot Text Annotations

O0_IP3R_cell1_tot Universal ID's

O0_IP3R_cell1_tot Text Annotations

Applications

Name
Properties Math Type
Annotation
Deterministic 1 Specs - Species
Specs - Reaction
Simulations 		Deterministic (ODE) Compartmental
Deterministic 2 Specs - Species
Specs - Reaction
Simulations 		Deterministic (ODE) Compartmental (copied from Deterministic 1)

Deterministic 1 Universal ID's

Deterministic 1 Text Annotations

Deterministic 2 Universal ID's

Deterministic 2 Text Annotations

Specifications (Species) - Deterministic 1 go to Simulations

Species
Initial Condition
Diffusion Constant
Structure
Ca_cell1 0.3 [umol] 0.0 [m2/s] Cytosol
IP3R_cell1 0.8 [umol] 0.0 [m2/s] Cytosol

Specifications (Reaction) - Deterministic 1 go to Simulations

Name
Enabled?
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 go to Specifications

Name
End Time
Output Options
Simulation1 30.0

KeepEvery 1

KeepAtMost 1000

Deterministic 1 Universal ID's

Deterministic 1 Text Annotations

Assignments

Name Variable Assignment Function Expression

Events

Name Trigger Type Variable Assignment

Geometry Compartmental2132244465

(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

Events

Name Variable Rate Expression

Specifications (Species) - Deterministic 2 go to Simulations

Species
Initial Condition
Diffusion Constant
Structure
Ca_cell1 0.3 [umol] 0.0 [m2/s] Cytosol
IP3R_cell1 0.8 [umol] 0.0 [m2/s] Cytosol

Specifications (Reaction) - Deterministic 2 go to Simulations

Name
Enabled?
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 go to Specifications

Name
End Time
Output Options
Simulation1_1 30.0

KeepEvery 1

KeepAtMost 1000

Deterministic 2 Universal ID's

Deterministic 2 Text Annotations

Assignments

Name Variable Assignment Function Expression

Events

Name Trigger Type Variable Assignment

Geometry Compartmental1280423882

(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

Events

Name Variable Rate Expression

Global Parameters

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]

Universal ID's

Text Annotations

Universal ID's

Text Annotations

Universal ID's

Text Annotations

Universal ID's

Text Annotations

Universal ID's

Text Annotations

Universal ID's

Text Annotations

Universal ID's

Text Annotations

Universal ID's

Text Annotations

Universal ID's

Text Annotations

Universal ID's

Text Annotations

Universal ID's

Text Annotations

Universal ID's

Text Annotations

Downloads

Model Format
Model Downloads
Virtual Cell Markup Language VCML File
PDF Report Report
COMBINE Archive OMEX File
SEDML SEDML File
File Format
Application Downloads
BNGL Deterministic 1.bngl , Deterministic 2.bngl
SBML Deterministic 1.sbml , Deterministic 2.sbml
Matlab Deterministic 1.m , Deterministic 2.m
NFSim XML Deterministic 1.xml , Deterministic 2.xml