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
wc_lang.core.DfbaObjective.reaction_rate_units
wc_lang.core.DfbaObjReaction.units

time-1

s-1,

wc_lang.core.ReactionRateUnit

Reaction flux bounds

wc_lang.core.Reaction.flux_min
wc_lang.core.Reaction.flux_max
wc_lang.core.Reaction.flux_bound_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
wc_lang.core.DfbaObjective.coefficient_units

time

s

wc_lang.core.DfbaObjectiveCoefficientUnit

dFBA objective species

wc_lang.core.DfbaObjSpecies.value
wc_lang.core.DfbaObjSpecies.units
volume^-1 time^-1,
gDCW^-1 time^-1
M s^-1
mol gDCW^-1 s^-1

wc_lang.core.DfbaObjSpeciesUnit

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