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CompartmentalModeling

Guides

  • Compartmental Modeling

Tech Notes

  • Vertical Transmission Models

Symbols

  • DynamicTransmissionModel
  • ForceOfInfection
  • Incidence
  • NextGenerationMatrix
  • CollectModel
  • CompartmentalModelGraph
  • CompetitiveInhibitorKinetics
  • DefinePropensityFunction
  • DeriveTransitions
  • DynamicTransmissionModel
  • EnzymeReaction
  • EpidemiologyModelData
  • EpidemiologyModel
  • ExpandModel
  • ForceOfInfection
  • HillKinetics
  • Incidence
  • KineticCompartmentalModel
  • KineticReactionNetworkModel
  • MichaelisMentenKinetics
  • NextGenerationMatrix
  • NoncompetitiveInhibitorKinetics
  • NullCompartment
  • ResolveCompartmentalModel
  • StochasticSolve
  • StoichiometryTable
  • StratifyModel
  • Transition
  • UncompetitiveInhibitorKinetics
  • VitalDemographicsModel
  • $C
  • $CompartmentalModelingVersion
  • $EpidemiologyColor
  • $EpidemiologyModelingVersion
  • $R
  • $SystemsBiologyModelingVersion
RobertNachbar`SystemsBiologyModeling`
EnzymeReaction
​
EnzymeReaction
[sub,{
ks
a
,
ks
d
},enz,
kp
d
,prod]
returns a list of three transitions for the conversion of substrate
sub
by enzyme
enz
to product
prod
, with substrate association and dissociation rates
ks
a
and
ks
d
, and enzyme-substrate complex breakdown rate to product
kp
d
.
​
​
EnzymeReaction
[sub,{
ks
a
,
ks
d
},enz,{
kp
d
,
kp
a
},prod]
returns a list of four transitions for the reversible conversion of substrate
sub
by enzyme
enz
to product
prod
, with substrate association and dissociation rates
ks
a
and
ks
d
, and product dissociation and association rates
kp
d
and
kp
a
.
​
Details and Options

Examples  
(5)
Basic Examples  
(2)
Generate the three
Transition
objects for an enzyme reaction:
In[1]:=
model=
EnzymeReaction
[,{
k
a
,
k
d
},ℰ,
k
p
,]
Out[1]=
ℰ+
k
a
→
ℰ·,ℰ·
k
d
→
ℰ+,ℰ·
k
p
→
ℰ+
Show the compartmental model graph as a Petri net:
In[2]:=
CompartmentalModelGraph
model,"GraphTheme""PetriNet",
options

Out[2]=
​
Generate the
Transition
objects for a reversible enzyme reaction:
In[1]:=
model=
EnzymeReaction
[,{
k
a
,
k
d
},ℰ,{
kp
d
,
kp
a
},]
Out[1]=
ℰ+
k
a
→
ℰ·,ℰ·
k
d
→
ℰ+,ℰ·
kp
d
→
ℰ+,ℰ+
kp
a
→
ℰ·
Show the compartmental model graph as a Petri net:
In[2]:=
CompartmentalModelGraph
model,"GraphTheme""PetriNet",
options

Out[2]=
Options  
(1)

Applications  
(2)

SeeAlso
Transition
 
▪
MichaelisMentenKinetics
 
▪
HillKinetics
 
▪
CompetitiveInhibitorKinetics
 
▪
NoncompetitiveInhibitorKinetics
 
▪
UncompetitiveInhibitorKinetics
 
▪
KineticReactionNetworkModel
 
▪
CenterDot
 
▪
AngleBracket
RelatedGuides
▪
Compartmental Modeling
""

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