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. Global Configuration
  • 1.1. The configuration object
  • 1.2. Reaction bounds
  • 1.3. Solver
• 2. Building a Model
  • 2.1. Model, Reactions and Metabolites
  • 2.2. Objective
  • 2.3. Model Validation
  • 2.4. Exchanges, Sinks and Demands
• 3. Reading and Writing Models
  • 3.1. SBML
  • 3.2. JSON
  • 3.3. YAML
  • 3.4. MATLAB
  • 3.5. Pickle
• 4. Simulating with FBA
  • 4.1. Running FBA
  • 4.2. Changing the Objectives
  • 4.3. Running FVA
  • 4.4. Running pFBA
  • 4.5. Running geometric FBA
• 5. Simulating Deletions
  • 5.1. Knocking out single genes and reactions
  • 5.2. Single Deletions
  • 5.3. Double Deletions
  • 5.4. Accessing individual deletion results
• 6. Production envelopes
• 7. Flux sampling
  • 7.1. Basic usage
  • 7.2. Advanced usage
  • 7.3. Adding constraints
• 8. Loopless FBA
  • 8.1. Loopless solution
  • 8.2. Loopless model
  • 8.3. Method
• 9. Consistency testing
  • 9.1. Using FVA
  • 9.2. Using FASTCC
• 10. Gapfillling
• 11. Growth media
  • 11.1. Minimal media
  • 11.2. Boundary reactions
• 12. Solvers
  • 12.1. Internal solver interfaces
• 13. Tailored constraints, variables and objectives
  • 13.1. Constraints
  • 13.2. Objectives
  • 13.3. Variables
• 14. Dynamic Flux Balance Analysis (dFBA) in COBRApy
  • 14.1. Set up the dynamic system
  • 14.2. Run the dynamic FBA simulation
• 15. Using the COBRA toolbox with cobrapy
• 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 Reference
  • 17.1. cobra
  • 17.2. test_room
  • 17.3. test_geometric
  • 17.4. test_parsimonious
  • 17.5. test_reaction
  • 17.6. test_gapfilling
  • 17.7. test_variability
  • 17.8. test_fastcc
  • 17.9. test_moma
  • 17.10. conftest
  • 17.11. test_loopless
  • 17.12. test_deletion
  • 17.13. test_phenotype_phase_plane
  • 17.14. update_pickles
  • 17.15. test_util
  • 17.16. test_array
  • 17.17. test_context
  • 17.18. test_process_pool
  • 17.19. test_solver
  • 17.20. test_notes
  • 17.21. test_json
  • 17.22. test_annotation_format
  • 17.23. test_mat
  • 17.24. test_annotation
  • 17.25. test_sbml
  • 17.26. test_yaml
  • 17.27. test_io_order
  • 17.28. test_pickle
  • 17.29. test_load
  • 17.30. test_metabolite_summary
  • 17.31. test_model_summary
  • 17.32. test_reaction_summary
  • 17.33. test_boundary_types
  • 17.34. test_minimal_medium
  • 17.35. test_group
  • 17.36. test_configuration
  • 17.37. test_solution
  • 17.38. test_dictlist
  • 17.39. test_core_reaction
  • 17.40. test_model
  • 17.41. test_metabolite
  • 17.42. test_gene
  • 17.43. test_optgp
  • 17.44. test_achr
  • 17.45. test_sampling

Indices and tables

• Index

• Module Index

• Search Page