reconstruction.ecoli.simulation_data

SimulationData for Ecoli

Raw data processed into forms convenient for whole-cell modeling

class reconstruction.ecoli.simulation_data.SimulationDataEcoli[source]

Bases: object

_add_base_codes(raw_data)[source]
_add_compartment_keys(raw_data)[source]
_add_condition_data(raw_data)[source]
_add_molecular_weight_keys(raw_data)[source]
adjust_final_expression(gene_indices, factors)[source]
calculate_ppgpp_expression(condition)[source]

Calculates the expected expression of RNA based on ppGpp regulation in a given condition and the expected transcription factor effects in that condition.

Relies on other values that are calculated in the fitting process so should only be called after the parca has been run.

Parameters:

condition (str) – label for the desired condition to calculate the average expression for (eg. ‘basal’, ‘with_aa’, etc)

initialize(raw_data, basal_expression_condition='M9 Glucose minus AAs')[source]