Physiology

Reaction Diagram

reactionDiagram

Cross-References

Annotations

Reactions

Reactions
Name
Structure
Kinetics
Depiction
PKA_B_Unnamed_compartment+C_Unnamed_compartmentPKA_B_C_Unnamed_compartment r2 Unnamed compartment MassAction
cAMP_Unnamed_compartment+PKA_2C_Unnamed_compartmentPKA_B_C2_Unnamed_compartment reaction11 Unnamed compartment MassAction
cAMP_Unnamed_compartment+PKA_B_C_Unnamed_compartmentPKA_BB_A_C_Unnamed_compartment reaction17 Unnamed compartment MassAction
PKA_BB_A_Unnamed_compartment+C_Unnamed_compartmentPKA_BB_A_C_Unnamed_compartment r3 Unnamed compartment MassAction
PKA_Unnamed_compartment+cAMP_Unnamed_compartmentPKA_B_Unnamed_compartment reaction21 Unnamed compartment MassAction
C_Unnamed_compartment+PKA_B_C_Unnamed_compartmentPKA_B_C2_Unnamed_compartment r1 Unnamed compartment MassAction
cAMP_Unnamed_compartment+PKA_B_Unnamed_compartmentPKA_BB_A_Unnamed_compartment reaction22 Unnamed compartment MassAction
C_Unnamed_compartment+PKA_Unnamed_compartmentPKA_C_Unnamed_compartment reaction5 Unnamed compartment MassAction
cAMP_Unnamed_compartment+PKA_C_Unnamed_compartmentPKA_B_C_Unnamed_compartment reaction6 Unnamed compartment MassAction
PKA_C_Unnamed_compartment+C_Unnamed_compartmentPKA_2C_Unnamed_compartment reaction0 Unnamed compartment MassAction

Structures

Name
Type
Electrical
Unnamed compartment Compartment (+)   (-)

Species

Name
Structure
BioNetGen Definition
Depiction
PKA_Unnamed_compartment Unnamed compartment Unnamed compartment
PKA_B_C2_Unnamed_compartment Unnamed compartment Unnamed compartment
PKA_B_Unnamed_compartment Unnamed compartment Unnamed compartment
PKA_B_C_Unnamed_compartment Unnamed compartment Unnamed compartment
PKA_BB_A_C_Unnamed_compartment Unnamed compartment Unnamed compartment
C_Unnamed_compartment Unnamed compartment Unnamed compartment
PKA_C_Unnamed_compartment Unnamed compartment Unnamed compartment
PKA_2C_Unnamed_compartment Unnamed compartment Unnamed compartment
PKA_BB_A_Unnamed_compartment Unnamed compartment Unnamed compartment
cAMP_Unnamed_compartment Unnamed compartment Unnamed compartment

Molecules

Name
BioNetGen Definition
DEPICTION

Observables

Name
Structure
Count
BNGL Definition
Sequence Type
DEPICTION

Applications

Name
Properties Math Type
Annotation
test Specs - Species
Specs - Reaction
Simulations
Deterministic (ODE) Compartmental

Specifications (Species) - test go to Simulations

Species
Initial Condition
Diffusion Constant
Structure
PKA_Unnamed_compartment 0.0125 [uM] 0.0 [um2/s] Unnamed compartment
PKA_B_C2_Unnamed_compartment 0.0 [uM] 0.0 [um2/s] Unnamed compartment
PKA_B_Unnamed_compartment 0.0 [uM] 0.0 [um2/s] Unnamed compartment
PKA_B_C_Unnamed_compartment 0.0 [uM] 0.0 [um2/s] Unnamed compartment
PKA_BB_A_C_Unnamed_compartment 0.0 [uM] 0.0 [um2/s] Unnamed compartment
C_Unnamed_compartment 5.025 [uM] 0.0 [um2/s] Unnamed compartment
PKA_C_Unnamed_compartment 0.0 [uM] 0.0 [um2/s] Unnamed compartment
PKA_2C_Unnamed_compartment 0.0 [uM] 0.0 [um2/s] Unnamed compartment
PKA_BB_A_Unnamed_compartment 0.0 [uM] 0.0 [um2/s] Unnamed compartment
cAMP_Unnamed_compartment 0.0 [uM] 0.0 [um2/s] Unnamed compartment

Specifications (Reaction) - test go to Simulations

Name
Enabled?
r2 included
reaction11 included
reaction17 included
r3 included
reaction21 included
r1 included
reaction22 included
reaction5 included
reaction6 included
reaction0 included

Simulations - test go to Specifications

Name
End Time
Output Options
Simulation0 1200.0

KeepEvery 20

KeepAtMost 6000

Copy of Simulation0 500000.0

KeepEvery 20

KeepAtMost 6000

Copy of Copy of Simulation0 500000.0

KeepEvery 20

KeepAtMost 6000

Assignments

Name Variable Assignment Function Expression

Events

Name Trigger Type Variable Assignment

Geometry non-spatial1833399091

(Origin: 0.0, 0.0, 0.0; Extent: 10.0, 10.0, 10.0 [um])

Dimension Type Subdomain Adjacent Subvolumes Size Mapped Compartment
Compartmental Compartment Unnamed compartment

Events

Name Variable Rate Expression

Global Parameters

Name
Expression
F_B_binding 0.003175[uM-1.s-1]
B_kd 9.7E-4[tbd]
B_factor 5.0[tbd]
F_A_binding 0.003[uM-1.s-1]
A_kd 53.199999999999996[tbd]
A_factor 23.0[tbd]
C_kr 0.0023[s-1]
C_kd 3.27E-8[uM]
Vm 0.31[s-1]
Kf_A 0.08[1]
Kr_A 0.012[s-1]
Kf_B 0.082[1]
Kr_B 2.21E-4[s-1]
B1_factor 1.0[tbd]
A1_factor 226.0[tbd]
A2_factor 151.0[tbd]
B2_factor 602.0[tbd]
A2_kd 0.002[tbd]
spots 2.0[uM]
R_A_factor 1.0[tbd]
R_B_factor 1.0[tbd]
F1 1.0[tbd]
F2 1540.0[tbd]
F3 13.5[tbd]
F4 1550.0[tbd]
C_kd2 1.28E-5[tbd]
C_kr2 0.03[uM-1.s-1]
C_kr3 0.03[uM-1.s-1]
C_kr4 0.03[uM-1.s-1]
F5 8.27[tbd]
F9 2.288[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 test.bngl
SBML test.sbml
Matlab test.m
NFSim XML test.xml