Physiology

Reaction Diagram

reactionDiagram

Cross-References

Annotations

Reactions

Reactions
Name
Structure
Kinetics
Depiction
s4ms4m+Ca Ca_influx m0 MassAction
PDEa+cAMPPDEa cAMPdeg c0 MassAction
cAMP inddeg c0 MassAction
AC+CaACa AC act m0 MassAction
Ca+PDEPDEa PDEact c0 MassAction
PDE+cAMPPDE basedeg c0 MassAction
ACAC+cAMP baseAC m0 MassAction
ACacAMP+ACa ACactive m0 MassAction
Ca removeCa m0 MassAction
cAMP cAMPind m0 GeneralKinetics
s0ms0m r0m m1 MassAction
s0m+s4ms4m r1m m1 MassAction
s4m r2m m1 MassAction

Ca_influx Universal ID's

Ca_influx Text Annotations

cAMPdeg Universal ID's

cAMPdeg Text Annotations

inddeg Universal ID's

inddeg Text Annotations

AC act Universal ID's

AC act Text Annotations

PDEact Universal ID's

PDEact Text Annotations

basedeg Universal ID's

basedeg Text Annotations

baseAC Universal ID's

baseAC Text Annotations

ACactive Universal ID's

ACactive Text Annotations

removeCa Universal ID's

removeCa Text Annotations

cAMPind Universal ID's

cAMPind Text Annotations

r0m Universal ID's

r0m Text Annotations

r1m Universal ID's

r1m Text Annotations

r2m Universal ID's

r2m Text Annotations

Expressions for Ca_influx

reaction rate

J

((Kf * s4m) - ((Kr * s4m) * Ca)) [molecules.um-2.s-1]

inward current density

I

0.0 [pA.um-2]

net charge valence

netValence

1.0 [1]

forward rate constant

Kf

200.0 [s-1]

reverse rate constant

Kr

0.0 [s-1.uM-1]

Expressions for cAMPdeg

reaction rate

J

(((Kf * PDEa) * cAMP) - (Kr * PDEa)) [uM.s-1]

forward rate constant

Kf

100.0 [s-1.uM-1]

reverse rate constant

Kr

0.0 [s-1]

Expressions for inddeg

reaction rate

J

(Kf * cAMP) [uM.s-1]

forward rate constant

Kf

50.0 [s-1]

reverse rate constant

Kr

0.0 [uM.s-1]

Expressions for AC act

reaction rate

J

(((Kf * AC) * Ca) - (Kr * ACa)) [molecules.um-2.s-1]

inward current density

I

0.0 [pA.um-2]

net charge valence

netValence

1.0 [1]

forward rate constant

Kf

100.0 [s-1.uM-1]

reverse rate constant

Kr

100.0 [s-1]

Expressions for PDEact

reaction rate

J

(((Kf * Ca) * PDE) - (Kr * PDEa)) [uM.s-1]

forward rate constant

Kf

10.0 [s-1.uM-1]

reverse rate constant

Kr

100.0 [s-1]

Expressions for basedeg

reaction rate

J

(((Kf * PDE) * cAMP) - (Kr * PDE)) [uM.s-1]

forward rate constant

Kf

10.0 [s-1.uM-1]

reverse rate constant

Kr

0.0 [s-1]

Expressions for baseAC

reaction rate

J

((Kf * AC) - ((Kr * AC) * cAMP)) [molecules.um-2.s-1]

inward current density

I

0.0 [pA.um-2]

net charge valence

netValence

1.0 [1]

forward rate constant

Kf

10.0 [s-1]

reverse rate constant

Kr

0.0 [s-1.uM-1]

Expressions for ACactive

reaction rate

J

((Kf * ACa) - ((Kr * cAMP) * ACa)) [molecules.um-2.s-1]

inward current density

I

0.0 [pA.um-2]

net charge valence

netValence

1.0 [1]

forward rate constant

Kf

200.0 [s-1]

reverse rate constant

Kr

0.0 [s-1.uM-1]

Expressions for removeCa

reaction rate

J

(Kf * Ca) [molecules.um-2.s-1]

inward current density

I

0.0 [pA.um-2]

net charge valence

netValence

1.0 [1]

forward rate constant

Kf

1000.0 [molecules.um-2.s-1.uM-1]

reverse rate constant

Kr

0.0 [molecules.um-2.s-1]

Expressions for cAMPind

reaction rate

J

20.0 [molecules.um-2.s-1]

inward current density

I

0.0 [pA.um-2]

net charge valence

netValence

1.0 [1]

Expressions for r0m

reaction rate

J

((Kf * s0m) - (Kr * pow(s0m,2.0))) [molecules.um-2.s-1]

inward current density

I

0.0 [pA.um-2]

net charge valence

netValence

1.0 [1]

forward rate constant

Kf

1.0 [s-1]

reverse rate constant

Kr

0.0 [um2.s-1.molecules-1]

Expressions for r1m

reaction rate

J

(((Kf * s0m) * s4m) - (Kr * pow(s4m,2.0))) [molecules.um-2.s-1]

inward current density

I

0.0 [pA.um-2]

net charge valence

netValence

1.0 [1]

forward rate constant

Kf

1.0 [um2.s-1.molecules-1]

reverse rate constant

Kr

0.0 [um2.s-1.molecules-1]

Expressions for r2m

reaction rate

J

(Kf * s4m) [molecules.um-2.s-1]

inward current density

I

0.0 [pA.um-2]

net charge valence

netValence

1.0 [1]

forward rate constant

Kf

5.0 [s-1]

reverse rate constant

Kr

0.0 [molecules.um-2.s-1]

Structures

Name
Type
Electrical
m0 Membrane (+)   (-)
m1 Membrane (+)   (-)
m2 Membrane (+)   (-)
m3 Membrane (+)   (-)
centermem Membrane (+)   (-)
c2 Compartment (+)   (-)
c0 Compartment (+)   (-)
c1 Compartment (+)   (-)
c3 Compartment (+)   (-)

m0 Universal ID's

m0 Text Annotations

m1 Universal ID's

m1 Text Annotations

m2 Universal ID's

m2 Text Annotations

m3 Universal ID's

m3 Text Annotations

centermem Universal ID's

centermem Text Annotations

c2 Universal ID's

c2 Text Annotations

c0 Universal ID's

c0 Text Annotations

c1 Universal ID's

c1 Text Annotations

c3 Universal ID's

c3 Text Annotations

Species

Name
Structure
BioNetGen Definition
Depiction
Ca c0 c0
AC m0 m0
cAMP c0 c0
PDE c0 c0
ACa m0 m0
PDEa c0 c0
s0m m1 m1
s4m m1 m1

Ca Universal ID's

Ca Text Annotations

AC Universal ID's

AC Text Annotations

cAMP Universal ID's

cAMP Text Annotations

PDE Universal ID's

PDE Text Annotations

ACa Universal ID's

ACa Text Annotations

PDEa Universal ID's

PDEa Text Annotations

s0m Universal ID's

s0m Text Annotations

s4m Universal ID's

s4m Text Annotations

Molecules

Name
BioNetGen Definition
DEPICTION

Observables

Name
Structure
Count
BNGL Definition
Sequence Type
DEPICTION

Applications

Name
Properties Math Type
Annotation
Copy of Application0 1 Specs - Species
Specs - Reaction
Simulations 		Stochastic (SSA) Compartmental (copied from Application0)

Copy of Application0 1 Universal ID's

Copy of Application0 1 Text Annotations

Specifications (Species) - Copy of Application0 1 go to Simulations

Species
Initial Condition
Diffusion Constant
Structure
Ca 10.0 [molecules] 0.0 [um2/s] c0
cAMP 0.0 [molecules] 0.0 [um2/s] c0
PDE 45.0 [molecules] 0.0 [um2/s] c0
PDEa 5.0 [molecules] 0.0 [um2/s] c0
AC 0.0 [molecules] 0.0 [um2/s] m0
ACa 0.0 [molecules] 0.0 [um2/s] m0
s0m 0.0 [molecules] 0.0 [um2/s] m1
s4m 0.0 [molecules] 0.0 [um2/s] m1

Specifications (Reaction) - Copy of Application0 1 go to Simulations

Name
Enabled?
Ca_influx included
cAMPdeg included
inddeg included
AC act included
PDEact included
basedeg included
baseAC included
ACactive included
removeCa included
cAMPind included
r0m included
r1m included
r2m included

Simulations - Copy of Application0 1 go to Specifications

Name
End Time
Output Options
done 1 2 1 99.9

OutputTimeStep 0.1
double done 1 2 1 99.9

OutputTimeStep 0.1

Copy of Application0 1 Universal ID's

Copy of Application0 1 Text Annotations

Copy of Application0 1 Universal ID's

Copy of Application0 1 Text Annotations

Assignments

Name Variable Assignment Function Expression

Events

Name Trigger Type Variable Assignment

Geometry non-spatial1785237018

(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 centermem

Events

Name Variable Rate Expression

Global Parameters

Name
Expression
g0 (((2.0 * ((2.0 * floor((t / 4.0))) - floor((2.0 * t / 4.0)))) + 2.0) / 2.0)[molecules.um-2]

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 Copy of Application0 1.bngl
SBML Copy of Application0 1.sbml
Matlab Copy of Application0 1.m
NFSim XML Copy of Application0 1.xml