reconstruction.ecoli.simulation_data

SimulationData for Ecoli

Raw data processed into forms convenient for whole-cell modeling

class reconstruction.ecoli.simulation_data.SimulationDataEcoli

Bases: object

_add_base_codes(raw_data)

_add_compartment_keys(raw_data)

_add_condition_data(raw_data)

_add_molecular_weight_keys(raw_data)

adjust_final_expression(gene_indices, factors)

adjust_new_gene_final_expression(gene_indices, factors)

Adjusting the final expression values of new genes must be handled separately because the baseline new gene expression values need to be set to small non-zero values using data loaded from flat/new_gene_data/new_gene_baseline_expression_parameters.tsv, as new genes are knocked out by default.

Parameters:

• gene_indices – Indices of new genes to adjust

• factors – Multiplicative factor to adjust by

calculate_ppgpp_expression(condition)

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')