Documentation for COBRApy

For installation instructions, please see INSTALL.md.

Many of the examples below are viewable as IPython notebooks, which can be viewed at nbviewer.

• 1. Getting Started
  • 1.1. Reactions
  • 1.2. Metabolites
  • 1.3. Genes
• 2. Building a Model
• 3. Reading and Writing Models
  • 3.1. SBML
  • 3.2. JSON
  • 3.3. MATLAB
  • 3.4. Pickle
• 4. Simulating with FBA
  • 4.1. Running FBA
  • 4.2. Changing the Objectives
  • 4.3. Running FVA
  • 4.4. Running pFBA
• 5. Simulating Deletions
  • 5.1. Single Deletions
  • 5.2. Double Deletions
• 6. Phenotype Phase Plane
• 7. Mixed-Integer Linear Programming
  • 7.1. Ice Cream
  • 7.2. Restaurant Order
  • 7.3. Boolean Indicators
• 8. Quadratic Programming
• 9. Loopless FBA
• 10. Gapfillling
  • 10.1. GrowMatch
  • 10.2. SMILEY
• 11. Solver Interface
  • 11.1. Attributes and functions
  • 11.2. Example with FVA
• 12. Using the COBRA toolbox with cobrapy
• 13. FAQ
  • 13.1. How do I install cobrapy?
  • 13.2. How do I cite cobrapy?
  • 13.3. How do I rename reactions or metabolites?
  • 13.4. How do I delete a gene?
  • 13.5. How do I change the reversibility of a Reaction?
  • 13.6. How do I generate an LP file from a COBRA model?
  • 13.7. How do I visualize my flux solutions?
• 14. cobra package
  • 14.1. Subpackages
  • 14.2. Module contents

Indices and tables

• Index
• Module Index
• Search Page