PAModelpy 0.0.1

Python framework for building and analysing protein allocation models

PAMpy

Python implementation of the PAM framework (https://github.com/Spherotob/PAM_public) to create GECKO like ME models.

Code structure:

• example_PAM_generation: (in ./Examples/PAModel_example_script.ipynb) An example of how to build, run and validate a proteome allocation model for Escherichia coli.
• EnzymeSectors: The objects which are used to store the data of the different enzyme sectors which are added to the genome-scale model
• PAModel: Proteome Allocation (PA) model class. This class builds on to the cobra.core.Model class from the COBRApy toolbox with functions to build enzyme sectors, to add enzyme kinetics parameters and in the future to perform a sensitivity analysis on the enzyme variables.
• Enzyme: Different classes which relate enzymes to the model with enzyme constraints and variables.
• CatalyticEvent: A class which serves as an interface between reactions and enzyme. This allows for easy lookup of Protein-Reaction assocations.
• PAMValidator: Functions to validate the model predictions with physiology data and giving a graphical overview. The script uses data for E.coli (found in ./Data/Ecoli_physiology) by default.

Dependencies

cobrapy toolbox, Gurobi solver

More dependencies see pyproject.toml