impact.core.SingleTrial module¶

class impact.core.SingleTrial.SingleTrial¶

Bases: sqlalchemy.ext.declarative.api.Base

Container for TiterObject to build a whole trial out of different measurements. E.g. one flask would contain data for biomass (OD), products (ethanol, acetate), substrates (glucose), fluorescence (gfpmut3, mCherry)

Attributes

stages
trial_identifier

Methods

add_analyte_data(analyte_data)	Add a TiterObject
calculate()
calculate_ODE_fit()	WIP to fit the data to ODEs
calculate_mass_balance([OD_gdw, calculateFBACO2])	Calculate a mass balance given the supplied substrate and products
create_stage(stage_bounds)
link_identifiers(trial_identifier[, attrs])
normalize_data(normalize_to)
register_feature(feature)
serialize()
summary([print])

add_analyte_data(analyte_data)¶

Add a TiterObject

Parameters:	analyte_data : TiterObject A titer object to be added

analyte_dict¶

analyte_types = ['biomass', 'substrate', 'product']¶

calculate()¶

calculate_ODE_fit()¶

WIP to fit the data to ODEs

calculate_mass_balance(OD_gdw=None, calculateFBACO2=False)¶

Calculate a mass balance given the supplied substrate and products

Parameters:	OD_gdw : float The correlation betwen OD_gdw and OD600 calculateFBACO2 : bool Flag to calculate the CO2 using FBA (not implemented yet)

class_features = [<class 'impact.core.features.ProductYieldFactory'>, <class 'impact.core.features.SpecificProductivityFactory'>, <class 'impact.core.features.ODNormalizedDataFactory'>]¶

create_stage(stage_bounds)¶

id¶

link_identifiers(trial_identifier, attrs=['strain', 'media', 'environment'])¶

normalize_data(normalize_to)¶

parent_id¶

classmethod register_feature(feature)¶

serialize()¶

stage_indices¶

stage_parent_id¶

stages¶

summary(print=False)¶

trial_identifier¶

trial_identifier_id¶