Physiology

Reaction Diagram

reactionDiagram

Cross-References

Annotations

Reactions

Structures

Name
Type
Electrical
Cytosol Compartment (+)   (-)

Species

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

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
Deterministic 1 Specs - Species
Specs - Reaction
Simulations
Deterministic (ODE) Compartmental
Copy of Deterministic 1 Specs - Species
Specs - Reaction
Simulations
Deterministic (ODE) Compartmental

Specifications (Species) - Deterministic 1 go to Simulations

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

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

Copy of Simulation1 30.0

KeepEvery 1

KeepAtMost 1000

Copy of Copy of Simulation1 30.0

KeepEvery 1

KeepAtMost 1000

Copy of Copy of Copy of Simulation1 30.0

KeepEvery 1

KeepAtMost 1000

Specifications (Species) - Copy of Deterministic 1 go to Simulations

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

Specifications (Reaction) - Copy of 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 - Copy of Deterministic 1 go to Specifications

Name
End Time
Output Options
Simulation1_1 30.0

KeepEvery 1

KeepAtMost 1000

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

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BNGL
MatLab
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