Welcome to COBRAme’s documentation!

This resource is intended to:

1. Provide an overview of what ME-models are and how they work
2. Describe the architecture of the COBRAme code base.
3. Highlight the major object classes and how they interrelate
4. Demonstrate basic model building and editing procedures
5. Provide examples of how to query, edit and update information in a constructed ME-model

• 1. ME-model Fundamentals
  • 1.1. Coupling Constraints
  • 1.2. Biomass Dilution Constraints
• 2. COBRAme Software Architecture
  • 2.1. ProcessData
  • 2.2. MEReaction
  • 2.3. Overview
• 3. Building a ME-model
  • 3.1. Overview
  • 3.2. Initializing new ME-Models
  • 3.3. Adding Reactions without utility functions
  • 3.4. Adding Reactions using utility functions
• 4. Reaction Properties
  • 4.1. Metabolic Reactions
  • 4.2. Transcription Reactions
  • 4.3. Translation Reactions
  • 4.4. ComplexFormation Reactions
• 5. ME-model Saving and Loading
  • 5.1. As a full JSON file
  • 5.2. As a reduced JSON file
  • 5.3. As a pickle file
• 6. cobrame package
  • 6.1. Subpackages
  • 6.2. Module contents

Indices and tables

• Index
• Module Index
• Search Page