Physiology

Reaction Diagram

reactionDiagram

Cross-References

Annotations

Reactions

Structures

Name
Type
Electrical
Cytosol Compartment (+)   (-)

Species

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

Molecules

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

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

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)

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

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

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]

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