4.1. Units of WC models

Table 4.1 lists the units of each quantity in a WC model.

These units facilitate composition of multiple models of multiple cellular processes. In particular, these units represent dFBA models in volume (l) concentrations rather than in mass (gDCW) concentrations because this makes dFBA compatible with SSA and ODE models that are typically described in volume concentrations.

Table 4.1 Units of WC models.
Quantity Attributes Dimensions Units Units class
Time wc_lang.core.Model.time_units time s wc_lang.core.TimeUnit
Compartment density
wc_lang.core.Compartment.density
wc_lang.core.Compartment.density_units
mass / volume g l^-1 wc_lang.core.DensityUnit
Compartment volume
wc_lang.core.Compartment.volume
wc_lang.core.Compartment.volume_units
volume l^-1 wc_lang.core.VolumeUnit
Distribution of initial
concentration of a
species at the beginning
of the cell cycle
wc_lang.core.Concentration.distribution
wc_lang.core.Concentration.mean
wc_lang.core.Concentration.std
wc_lang.core.Concentration.units
molecule,
molecule volume-1
molecule,
M
wc_lang.core.ConcentrationUnit
Species count wc_lang.core.Species.units molecule molecule wc_lang.core.MoleculeCountUnit
Observable count
wc_lang.core.ObservableExpression.expression
wc_lang.core.Observable.units
molecule molecule wc_lang.core.MoleculeCountUnit
Observable coefficient wc_lang.core.ObservableExpression.expression dimensionless none wc_lang.core.ObservableCoefficientUnit
Reaction participant wc_lang.core.SpeciesCoefficient.coefficient dimensionless none wc_lang.core.ReactionParticipantUnit
Reaction rate
wc_lang.core.RateLawExpression.expression
wc_lang.core.RateLaw.units
SSA: time-1
other: volume-1 time-1
SSA: s-1,
Other: M s-1
wc_lang.core.ReactionRateUnit
Reaction flux
wc_lang.core.Reaction.flux_min
wc_lang.core.Reaction.flux_max
wc_lang.core.Reaction.flux_units
volume-1 time-1 M s^-1 wc_lang.core.ReactionFluxUnit
dFBA objective
wc_lang.core.DfbaObjectiveExpresssion.expression
wc_lang.core.DfbaObjective.units
time-1 s^-1 wc_lang.core.DfbaObjectiveUnit
dFBA objective coefficient wc_lang.core.DfbaObjectiveExpresssion.expression
Net reaction: time
Reaction: time volume
Net reaction: s
Reaction: s M^-1
wc_lang.core.DfbaObjectiveCoefficientUnit
dFBA net component
wc_lang.core.DfbaNetComponent.value
wc_lang.core.DfbaNetComponent.units
volume^-1 time^-1,
gDCW^-1 time^-1
M s^-1
mol gDCW^-1 s^-1
wc_lang.core.DfbaNetComponentUnit
dFBA net flux wc_lang.core.DfbaNetReaction.units time^-1 s-1 wc_lang.core.DfbaNetFluxUnit
Function
wc_lang.core.FunctionExpression.expression
wc_lang.core.Function.units
various various  
Parameter
wc_lang.core.Parameter.value
wc_lang.core.Parameter.units
various various  
Stop condition
wc_lang.core.StopCondition.expression
wc_lang.core.StopCondition.units
dimensionless none wc_lang.core.StopConditionUnit