PAModelpy 0.0.5.2

Python framework for building and analysing protein allocation models

PAModelpy - Protein Allocation Model reconstruction in Python

What is PAModelpy?

Models of metabolism are powerful tools to explore the metabolic potential of microorganism. Powerful tools have been created to support Python-based analysis of genome-scale models. These models, however, cannot capture all metabolic phenotypes and the simulation results have high flux variability. Adding protein to each reaction increases the simulation fidelity. The PAModelpy package is designed to integrate protein constraints and protein sectors as described by Alter et al. (2021) to metabolic models. It is the Python implementation of the PAM MATLAB framework to create GECKO like ME models.

The PAModelpy package builds upon the community-wide used COBRApy. We have extended this package with the following features:

• protein-reaction associations
• infrastructure to include isozymes and promiscuous enzymes
• protein sectors
• specialized objects to build protein allocation models
• the possibility to perform a computational efficient sensitivity analysis

Installation

IMPORTANT: PAModelpy is only compatible with Python >= 3.9 and <=3.11

PAModelpy is a PiPy package which allows for easy installation with pip:

pip install PAModelpy

Note that the package has been tested with the Gurobi solver. In order for Gurobi to work properly, please install gurobipy with a version matching your license.

For example for the version used for the development of PAModelpy:

pip install gurobipy==9.5.2

Code structure:

• 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

The dependencies of the PAModelpy package can be found in src/pyproject.toml. Because of the version of numpy used, the PAModelpy is only compatible with Python >= 3.9 and <=3.11.

License

Copyright institute of Applied Microbiology, RWTH Aachen University, Aachen, Germany (2023)

PAModelpy is released under both the GPL and LGPL licenses version 2 or later. You may choose which license you choose to use the software under.

This program is free software: you can redistribute it and/or modify it under the terms of the GNU General Public License or the GNU Lesser General Public License as published by the Free Software Foundation, either version 2 of the License, or (at your option) any later version.

This program is distributed in the hope that it will be useful, but WITHOUT ANY WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU General Public License for more details.