Welcome to the PAMparametrizer

The PAModelpy package is designed to integrate protein constraints and protein sectors into protein allocation models (PAMs). In this documentation, you can find all the information you need to parametrizer PAMs.

Table of Contents

• PAMparametrizer - parametrizing Protein Allocation Models with Flux Data
  • Why do we need a PAMparametrizer?
  • What does the PAMparametrizer do?
  • What can you find where in this repository?
  • Code structure
  • Dependencies
  • License
• Genetic Algorithm for Protein Allocation Model Parameter Estimation
  • Software Structure
  • Genetic Algorithm workflow
  • Fitness Evaluation adjustment
• Example usage of the PAMparametrizer
  • Example 1: Parametrizing the E. coli Protein Allocation Model with glucose as sole carbon source
  • Example 2: Parametrizing the E. coli Protein Allocation Model with multiple carbon sources
• Workflow for Protein Allocation Model Parameter Estimation
  • Software Structure
  • PAM parametrizer workflow
  • Data objects
• Parametrizing a PAM: from GEM to PAM
  • 1. The Genome-Scale Metabolic Model Sanity Check
  • 2. Building the Protein Sectors
  • 3. Design Choices
  • 4. Working with the PAMparametrizer
  • 5. Analyzing the Paramaterization Results
• API reference
  • PAM_parametrizer
  • genetic_algorithm_parametrization
  • utils