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
- 2. Building a Model
- 3. Reading and Writing Models
- 4. Simulating with FBA
- 5. Simulating Deletions
- 6. Production envelopes
- 7. Flux sampling
- 8. Loopless FBA
- 9. Consistency testing
- 10. Gapfillling
- 11. Growth media
- 12. Solvers
- 13. Tailored constraints, variables and objectives
- 14. Dynamic Flux Balance Analysis (dFBA) in COBRApy
- 15. Using the COBRA toolbox with cobrapy
- 16. FAQ
- 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
- 17.1.