loica.metabolism

Module Contents

Classes

DataMetabolism	Characterized context for gene expression, incorporates biomass and growth rate.
Metabolism	Context for gene expression, incorporates biomass and growth rate.
SimulatedMetabolism	Simulated context for gene expression, incorporates biomass and growth rate.

Functions

gompertz(t, y0, ymax, um, l)
gompertz_growth_rate(t, y0, ymax, um, l)
ramp_biomass(t, od0, start, slope)
ramp_growth_rate(t, start, slope)
step_biomass(t, od0, start)
step_growth_rate(t, start)

class DataMetabolism(name, fj, media, strain, vector, biomass_signal)

Bases: Metabolism

Characterized context for gene expression, incorporates biomass and growth rate. …

namestr, optional

Name of the metabolism or correponding strain

fjFlapjack

Flapjack instance used to fetch data from

mediastr

Name of the media to query

strainstr

Name of the strain to query

vectorstr

Name of the vector to query

biomass_signalstr

Name of signal to query and use as biomass

biomass(t)

Return biomass at a given time from characterization data

growth:rate(t)

Return growth rate at a given time from characterization data

biomass(self, t)

growth_rate(self, t)

class Metabolism(name=None)

Context for gene expression, incorporates biomass and growth rate. …

namestr, optional

Name of the metabolism or correponding strain

class SimulatedMetabolism(name, biomass, growth_rate)

Bases: Metabolism

Simulated context for gene expression, incorporates biomass and growth rate. …

namestr, optional

Name of the metabolism or correponding strain

biomass

A function of time that describes biomass f(t)=biomass

growth_rate

A function of time that describes the growth rate f(t)=growth rate

gompertz(t, y0, ymax, um, l)

gompertz_growth_rate(t, y0, ymax, um, l)

ramp_biomass(t, od0, start, slope)

ramp_growth_rate(t, start, slope)

step_biomass(t, od0, start)

step_growth_rate(t, start)