Documentation for COBRApy#

For installation instructions, please see INSTALL.rst.

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

• 1. Getting Started
  • 1.1. Loading a model and inspecting it
  • 1.2. Reactions
  • 1.3. Metabolites
  • 1.4. Genes
• 2. Global Configuration
  • 2.1. The configuration object
  • 2.2. Reaction bounds
  • 2.3. Solver
• 3. Building a Model
  • 3.1. Model, Reactions and Metabolites
  • 3.2. Objective
  • 3.3. Model Validation
  • 3.4. Exchanges, Sinks and Demands
• 4. Reading and Writing Models
  • 4.1. SBML
  • 4.2. JSON
  • 4.3. YAML
  • 4.4. MATLAB
  • 4.5. Pickle
• 5. Simulating with FBA
  • 5.1. Running FBA
  • 5.2. Changing the Objectives
  • 5.3. Running FVA
  • 5.4. Running pFBA
  • 5.5. Running geometric FBA
• 6. Simulating Deletions
  • 6.1. Knocking out single genes and reactions
  • 6.2. Single Deletions
  • 6.3. Double Deletions
  • 6.4. Accessing individual deletion results
• 7. Production envelopes
• 8. Flux sampling
  • 8.1. Basic usage
  • 8.2. Advanced usage
  • 8.3. Adding constraints
• 9. Loopless FBA
  • 9.1. Loopless solution
  • 9.2. Loopless model
  • 9.3. Method
• 10. Consistency testing
  • 10.1. Using FVA
  • 10.2. Using FASTCC
• 11. Gapfillling
• 12. Growth media
  • 12.1. Minimal media
  • 12.2. Boundary reactions
• 13. Solvers
  • 13.1. Internal solver interfaces
• 14. Tailored constraints, variables and objectives
  • 14.1. Constraints
  • 14.2. Objectives
  • 14.3. Variables
• 15. Dynamic Flux Balance Analysis (dFBA) in COBRApy
  • 15.1. Set up the dynamic system
  • 15.2. Run the dynamic FBA simulation
• 16. FAQ
  • 16.1. How do I install cobrapy?
  • 16.2. How do I cite cobrapy?
  • 16.3. How do I rename reactions or metabolites?
  • 16.4. How do I delete a gene?
  • 16.5. How do I change the reversibility of a Reaction?
  • 16.6. How do I generate an LP file from a COBRA model?
• 17. API
  • 17.1. Submodules
  • 17.2. Attributes
  • 17.3. Classes
  • 17.4. Functions
  • 17.5. Package Contents

Indices and tables#

• Index

• Module Index

• Search Page