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CHANGES.md
CHANGES.txt
CITATION.md
GETTING_STARTED.md
INSTALLATION.md
LICENSE
MANIFEST.in
Makefile
README.md
README.txt
TEST.md
TODO.md
VERSION
Vibrio ED002.features.txt
medialist.txt
new_cli_roles.txt
objects.inv
pyproject.toml
requirements.txt
setup.cfg
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PyFBA/__init__.py
PyFBA/version.py
PyFBA.egg-info/PKG-INFO
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PyFBA/Biochemistry/ModelSEEDDatabase/README.md
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PyFBA/Biochemistry/media/MOPS_NoC_L-Alanine.txt
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PyFBA/Biochemistry/media/MOPS_NoC_Myo-Inositol.txt
PyFBA/Biochemistry/media/MOPS_NoC_Negative_Control.txt
PyFBA/Biochemistry/media/MOPS_NoC_Oxalic_Acid.txt
PyFBA/Biochemistry/media/MOPS_NoC_Potassium_Sorbate.txt
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PyFBA/Biochemistry/media/MOPS_NoC_Putrescine.txt
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PyFBA/cmd/citation.py
PyFBA/cmd/entry.py
PyFBA/cmd/fba_from_reactions.py
PyFBA/cmd/fluxes.py
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PyFBA/cmd/gapfill_from_roles.py
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PyFBA/fba/create_stoichiometric_matrix.py
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PyFBA/fba/fluxes.py
PyFBA/fba/run_fba.py
PyFBA/filters/README.md
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PyFBA/filters/reactions_and_proteins.py
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PyFBA/gapfill/bisections.py
PyFBA/gapfill/ecnumbers.py
PyFBA/gapfill/essentials.py
PyFBA/gapfill/limit_reactions.py
PyFBA/gapfill/linked_reactions.py
PyFBA/gapfill/maps_to_proteins.py
PyFBA/gapfill/media.py
PyFBA/gapfill/orphan_compound.py
PyFBA/gapfill/probability.py
PyFBA/gapfill/reaction_minimization.py
PyFBA/gapfill/roles.py
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PyFBA/logs/formatting.py
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PyFBA/lp/glpk_solver.py
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PyFBA/metabolism/compound.py
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PyFBA/util/From_functional_roles_to_gap-filling.py
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PyFBA/util/createGrowthMediaList.py
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docs/_static/PyFBA.png
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example_code/RAST_neighboring_roles.py
example_code/__init__.py
example_code/find_reactions_by_compound.py
example_code/find_roles_by_compound.py
example_code/group_reactions.py
example_code/rast_annotations_to_reactions.py
example_code/reaction_info.py
example_code/reaction_statistics.py
example_code/run_fba_sbml.py
example_code/sbml_to_fba.py
example_code/statistics.py
example_code/test_individual_reactions.py
example_data/Citrobacter/Citrobacter_sedlakii.sbml
example_data/Citrobacter/Citrobacter_sedlakii_reactions.txt
example_data/Citrobacter/README.md
example_data/Citrobacter/ungapfilled_model/README.md
example_data/Citrobacter/ungapfilled_model/citrobacter.assigned_functions
example_data/Citrobacter/ungapfilled_model/citrobacter.reactions
example_data/Citrobacter/ungapfilled_model/citrobacter.roles
example_data/Citrobacter/ungapfilled_model/closest.genomes
example_data/Citrobacter/ungapfilled_model/closest.genomes.roles
iPythonNotebooks/Find a metabolite.ipynb
iPythonNotebooks/From_functional_roles_to_gap-filling.ipynb
iPythonNotebooks/Gap-fill_a_model.ipynb
iPythonNotebooks/PATRIC to FBA.ipynb
iPythonNotebooks/Reconstruct SBML From Scratch.ipynb
iPythonNotebooks/Saving_and_loading_a_model.ipynb
iPythonNotebooks/Using_an_SBML_model.ipynb
iPythonNotebooks/img/patric_dl.png
iPythonNotebooks/img/patric_ft.png
images/PyFBA.xcf
src/pyfba_assigned_functions.py
src/pyfba_sbml.py