geckopy.experimental

Submodules

• geckopy.experimental.experimental
• geckopy.experimental.molecular_weights
• geckopy.experimental.relaxation

Package Contents

Functions

limit_proteins(model: cobra.Model, measurements: pandas.DataFrame)	Apply proteomics measurements to model.
from_mmol_gDW(model: cobra.Model, processed_proteomics: pandas.DataFrame) → cobra.Model	Apply proteomics constraints to model and return the copied EC model.
from_copy_number(model: cobra.Model, index: pandas.Series, cell_copies: pandas.Series, stdev: pandas.Series, vol: float, dens: float, water: float) → cobra.Model	Convert cell_copies to mmol/gDW and apply them to model.

geckopy.experimental.limit_proteins(model: cobra.Model, measurements: pandas.DataFrame)

Apply proteomics measurements to model.

Adapted from https://github.com/DD-DeCaF/simulations/blob/devel/src/simulations/modeling/driven.py

Parameters

• model (cobra.Model (or geckopy.Model)) – The enzyme-constrained model.

• measurements (pd.DataFrame) – Protein abundances in mmol / gDW.

geckopy.experimental.from_mmol_gDW(model: cobra.Model, processed_proteomics: pandas.DataFrame) → cobra.Model

Apply proteomics constraints to model and return the copied EC model.

geckopy.experimental.from_copy_number(model: cobra.Model, index: pandas.Series, cell_copies: pandas.Series, stdev: pandas.Series, vol: float, dens: float, water: float) → cobra.Model

Convert cell_copies to mmol/gDW and apply them to model.