Physiology
Reaction Diagram
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(). | |
IP3R_cell1 | Cytosol | IP3R_cell1(Ca_bs!-,). |
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
Specifications (Reaction) - Deterministic 1 go to Simulations
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
Specifications (Reaction) - Deterministic 2 go to Simulations
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 |