Physiology

Reaction Diagram

reactionDiagram

Cross-References

Annotations

Reactions

Reactions
Name
Structure
Kinetics
Depiction
PKA_Unnamed_compartment+cAMP_Unnamed_compartmentPKA_B_Unnamed_compartment reaction21 Unnamed compartment MassAction
cAMP_Unnamed_compartment+PKA_A_B_C_Unnamed_compartmentPKA_BB_A_C_Unnamed_compartment reaction17 Unnamed compartment MassAction
PKA_BB_A_Unnamed_compartment+cAMP_Unnamed_compartmentPKA_AA_BB_Unnamed_compartment reaction8 Unnamed compartment MassAction
PKA_A_B_C_Unnamed_compartment+C_Unnamed_compartmentPKA_B_A_C2 r5 Unnamed compartment MassAction
cAMP_Unnamed_compartment+PKA_B_Unnamed_compartmentPKA_A_B_Unnamed_compartment reaction7 Unnamed compartment MassAction
C_Unnamed_compartment+PKA_B_C_Unnamed_compartmentPKA_B_C2_Unnamed_compartment r1 Unnamed compartment MassAction
cAMP_Unnamed_compartment+PKA_A_B_Unnamed_compartmentPKA_BB_A_Unnamed_compartment reaction22 Unnamed compartment MassAction
PKA_B_Unnamed_compartment+cAMP_Unnamed_compartmentPKA_B_B r7 Unnamed compartment MassAction
PKA_Unnamed_compartment+C_Unnamed_compartmentPKA_C_Unnamed_compartment reaction5 Unnamed compartment MassAction
PKA_2C_Unnamed_compartment+cAMP_Unnamed_compartmentPKA_B_C2_Unnamed_compartment reaction11 Unnamed compartment MassAction
PKA_B_C2_Unnamed_compartment+cAMP_Unnamed_compartmentPKA_B_A_C2 r6 Unnamed compartment MassAction
PKA_B_Unnamed_compartment+C_Unnamed_compartmentPKA_B_C_Unnamed_compartment r2 Unnamed compartment MassAction
PKA_C_Unnamed_compartment+C_Unnamed_compartmentPKA_2C_Unnamed_compartment reaction0 Unnamed compartment MassAction
PKA_AA_BB_Unnamed_compartment+C_Unnamed_compartmentPKA_AA_BB_C r0 Unnamed compartment MassAction
cAMP_Unnamed_compartment+PKA_C_Unnamed_compartmentPKA_B_C_Unnamed_compartment reaction6 Unnamed compartment MassAction
PKA_BB_A_Unnamed_compartment+C_Unnamed_compartmentPKA_BB_A_C_Unnamed_compartment r3 Unnamed compartment MassAction
cAMP_Unnamed_compartment+PKA_BB_A_C_Unnamed_compartmentPKA_AA_BB_C r4 Unnamed compartment MassAction
C_Unnamed_compartment+PKA_A_B_Unnamed_compartmentPKA_A_B_C_Unnamed_compartment reaction4 Unnamed compartment MassAction
PKA_B_B+cAMP_Unnamed_compartmentPKA_BB_A_Unnamed_compartment r8 Unnamed compartment MassAction
cAMP_Unnamed_compartment+PKA_B_C_Unnamed_compartmentPKA_A_B_C_Unnamed_compartment reaction18 Unnamed compartment MassAction

Structures

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

Species

Name
Structure
BioNetGen Definition
Depiction
cAMP_Unnamed_compartment Unnamed compartment Unnamed compartment
PKA_B_B Unnamed compartment Unnamed compartment
PKA_A_B_C_Unnamed_compartment Unnamed compartment Unnamed compartment
PKA_BB_A_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
PKA_C_Unnamed_compartment Unnamed compartment Unnamed compartment
PKA_Unnamed_compartment Unnamed compartment Unnamed compartment
PKA_A_B_Unnamed_compartment Unnamed compartment Unnamed compartment
PKA_2C_Unnamed_compartment Unnamed compartment Unnamed compartment
PKA_AA_BB_C Unnamed compartment Unnamed compartment
C_Unnamed_compartment Unnamed compartment Unnamed compartment
PKA_B_C2_Unnamed_compartment Unnamed compartment Unnamed compartment
PKA_B_A_C2 Unnamed compartment Unnamed compartment
PKA_AA_BB_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
cAMP_Unnamed_compartment 0.0 [uM] 0.0 [um2/s] Unnamed compartment
PKA_B_B 0.0 [uM] 0.0 [um2/s] Unnamed compartment
PKA_A_B_C_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
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
PKA_C_Unnamed_compartment 0.0 [uM] 0.0 [um2/s] Unnamed compartment
PKA_Unnamed_compartment 0.011 [uM] 0.0 [um2/s] Unnamed compartment
PKA_A_B_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_AA_BB_C 0.0 [uM] 0.0 [um2/s] Unnamed compartment
C_Unnamed_compartment 0.02 [uM] 0.0 [um2/s] Unnamed compartment
PKA_B_C2_Unnamed_compartment 0.0 [uM] 0.0 [um2/s] Unnamed compartment
PKA_B_A_C2 0.0 [uM] 0.0 [um2/s] Unnamed compartment
PKA_AA_BB_Unnamed_compartment 0.0 [uM] 0.0 [um2/s] Unnamed compartment

Specifications (Reaction) - test go to Simulations

Name
Enabled?
reaction21 included
reaction17 included
reaction8 included
r5 included
reaction7 included
r1 included
reaction22 included
r7 included
reaction5 included
reaction11 included
r6 included
r2 included
reaction0 included
r0 included
reaction6 included
r3 included
r4 included
reaction4 included
r8 included
reaction18 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

C_kr=.23 1200.0

KeepEvery 20

KeepAtMost 6000

C_kr=23 1200.0

KeepEvery 20

KeepAtMost 6000

C_kd=.0038 1200.0

KeepEvery 20

KeepAtMost 6000

C_kd=.000038 1200.0

KeepEvery 20

KeepAtMost 6000

Kf_A=.8 1200.0

KeepEvery 20

KeepAtMost 6000

Kf_A=.008 1200.0

KeepEvery 20

KeepAtMost 6000

Kr_A=.12 1200.0

KeepEvery 20

KeepAtMost 6000

Kr_A=.0012 1200.0

KeepEvery 20

KeepAtMost 6000

Kf_B=.82 1200.0

KeepEvery 20

KeepAtMost 6000

Kf_B=.0082 1200.0

KeepEvery 20

KeepAtMost 6000

Kr_B=.00221 1200.0

KeepEvery 20

KeepAtMost 6000

Kr_B=.0000221 1200.0

KeepEvery 20

KeepAtMost 6000

Copy of Kr_B=.0000221 1200.0

KeepEvery 20

KeepAtMost 6000

F_B_binding=31.75 1200.0

KeepEvery 20

KeepAtMost 6000

F_B_binding=.3175 1200.0

KeepEvery 20

KeepAtMost 6000

B_factor=50 1200.0

KeepEvery 20

KeepAtMost 6000

B_factor=.5 1200.0

KeepEvery 20

KeepAtMost 6000

B_kd=.13 1200.0

KeepEvery 20

KeepAtMost 6000

B_kd=.0013 1200.0

KeepEvery 20

KeepAtMost 6000

A_kd=.3 1200.0

KeepEvery 20

KeepAtMost 6000

A_kd=.003 1200.0

KeepEvery 20

KeepAtMost 6000

F_A_binding=3 1200.0

KeepEvery 20

KeepAtMost 6000

F_A_binding=.03 2000.0

KeepEvery 20

KeepAtMost 6000

A_Factor=230 2000.0

KeepEvery 20

KeepAtMost 6000

A_Factor=2.3 2000.0

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 0.0031[uM-1.s-1]
B_kd 6.59E-4[tbd]
B_factor 5.0[tbd]
F_A_binding 3.0[uM-1.s-1]
A_kd 0.00105[tbd]
A_factor 23.0[tbd]
C_kr 0.0023[s-1]
C_kd 2.52E-7[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]
F1 1.0[tbd]
F2 2310.0[tbd]
F3 13.5[tbd]
F4 206.0[tbd]
C_kd2 1.4E-6[tbd]
F5 275.0[tbd]
C_kr1 1.0[uM-1.s-1]
C_kr2 1.0[uM-1.s-1]
C_kr3 1.0[uM-1.s-1]
C_kr4 300.0[uM-1.s-1]
C_kr5 1.0[uM-1.s-1]
F6 1408.0[tbd]
F7 1380.0[tbd]
F9 1.97[tbd]
A2_kd 0.0057[uM]

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