CHANGES.md
CHANGES.txt
CITATION.md
GETTING_STARTED.md
INSTALLATION.md
LICENSE
MANIFEST.in
README.md
README.txt
TEST.md
TODO.md
VERSION
requirements.txt
setup.cfg
setup.py
PyFBA/__init__.py
PyFBA/version.py
PyFBA.egg-info/PKG-INFO
PyFBA.egg-info/SOURCES.txt
PyFBA.egg-info/dependency_links.txt
PyFBA.egg-info/entry_points.txt
PyFBA.egg-info/requires.txt
PyFBA.egg-info/top_level.txt
PyFBA.egg-info/zip-safe
PyFBA/Biochemistry/__init__.py
PyFBA/Biochemistry/ModelSEEDDatabase/ModelSEEDLICENSE.txt
PyFBA/Biochemistry/ModelSEEDDatabase/README.md
PyFBA/Biochemistry/ModelSEEDDatabase/__init__.py
PyFBA/Biochemistry/ModelSEEDDatabase/Annotations/Complexes.tsv
PyFBA/Biochemistry/ModelSEEDDatabase/Annotations/Roles.tsv
PyFBA/Biochemistry/ModelSEEDDatabase/Annotations/__init__.py
PyFBA/Biochemistry/ModelSEEDDatabase/Biochemistry/__init__.py
PyFBA/Biochemistry/ModelSEEDDatabase/Biochemistry/compounds.json
PyFBA/Biochemistry/ModelSEEDDatabase/Biochemistry/reactions.json
PyFBA/Biochemistry/ModelSEEDDatabase/Templates/__init__.py
PyFBA/Biochemistry/ModelSEEDDatabase/Templates/Core/Reactions.tsv
PyFBA/Biochemistry/ModelSEEDDatabase/Templates/Core/__init__.py
PyFBA/Biochemistry/ModelSEEDDatabase/Templates/Fungi/Reactions.tsv
PyFBA/Biochemistry/ModelSEEDDatabase/Templates/Fungi/__init__.py
PyFBA/Biochemistry/ModelSEEDDatabase/Templates/GramNegative/Reactions.tsv
PyFBA/Biochemistry/ModelSEEDDatabase/Templates/GramNegative/__init__.py
PyFBA/Biochemistry/ModelSEEDDatabase/Templates/GramPositive/Reactions.tsv
PyFBA/Biochemistry/ModelSEEDDatabase/Templates/GramPositive/__init__.py
PyFBA/Biochemistry/ModelSEEDDatabase/Templates/Microbial/Reactions.tsv
PyFBA/Biochemistry/ModelSEEDDatabase/Templates/Microbial/__init__.py
PyFBA/Biochemistry/ModelSEEDDatabase/Templates/Mycobacteria/Reactions.tsv
PyFBA/Biochemistry/ModelSEEDDatabase/Templates/Mycobacteria/__init__.py
PyFBA/Biochemistry/SEED/__init__.py
PyFBA/Biochemistry/SEED/Subsystems/SS_functions.txt
PyFBA/Biochemistry/SEED/Subsystems/__init__.py
PyFBA/Biochemistry/media/ArgonneLB.txt
PyFBA/Biochemistry/media/MOPS_NoC_2-Deoxy-D-Ribose.txt
PyFBA/Biochemistry/media/MOPS_NoC_4-Hydroxy-Phenylacetate.txt
PyFBA/Biochemistry/media/MOPS_NoC_Acetic_Acid.txt
PyFBA/Biochemistry/media/MOPS_NoC_Adenosine.txt
PyFBA/Biochemistry/media/MOPS_NoC_Adonitol.txt
PyFBA/Biochemistry/media/MOPS_NoC_Alpha-D-Glucose.txt
PyFBA/Biochemistry/media/MOPS_NoC_Alpha-D-Lactose.txt
PyFBA/Biochemistry/media/MOPS_NoC_Cellobiose.txt
PyFBA/Biochemistry/media/MOPS_NoC_Citric_Acid.txt
PyFBA/Biochemistry/media/MOPS_NoC_D-Alanine.txt
PyFBA/Biochemistry/media/MOPS_NoC_D-Arabinose.txt
PyFBA/Biochemistry/media/MOPS_NoC_D-Arabitol.txt
PyFBA/Biochemistry/media/MOPS_NoC_D-Asparagine.txt
PyFBA/Biochemistry/media/MOPS_NoC_D-Aspartic_Acid.txt
PyFBA/Biochemistry/media/MOPS_NoC_D-Cysteine.txt
PyFBA/Biochemistry/media/MOPS_NoC_D-Fructose.txt
PyFBA/Biochemistry/media/MOPS_NoC_D-Galactose.txt
PyFBA/Biochemistry/media/MOPS_NoC_D-Glucosamine.txt
PyFBA/Biochemistry/media/MOPS_NoC_D-Glucose-6-phosphate.txt
PyFBA/Biochemistry/media/MOPS_NoC_D-Glucose.txt
PyFBA/Biochemistry/media/MOPS_NoC_D-Glutamic_Acid.txt
PyFBA/Biochemistry/media/MOPS_NoC_D-Mannose.txt
PyFBA/Biochemistry/media/MOPS_NoC_D-Ribose.txt
PyFBA/Biochemistry/media/MOPS_NoC_D-Serine.txt
PyFBA/Biochemistry/media/MOPS_NoC_D-Xylose.txt
PyFBA/Biochemistry/media/MOPS_NoC_Dulcitol.txt
PyFBA/Biochemistry/media/MOPS_NoC_Erythritol.txt
PyFBA/Biochemistry/media/MOPS_NoC_Glycerol.txt
PyFBA/Biochemistry/media/MOPS_NoC_Glycine.txt
PyFBA/Biochemistry/media/MOPS_NoC_Inosine.txt
PyFBA/Biochemistry/media/MOPS_NoC_L-Alanine.txt
PyFBA/Biochemistry/media/MOPS_NoC_L-Arabinose.txt
PyFBA/Biochemistry/media/MOPS_NoC_L-Arabitol.txt
PyFBA/Biochemistry/media/MOPS_NoC_L-Asparagine.txt
PyFBA/Biochemistry/media/MOPS_NoC_L-Aspartic_Acid.txt
PyFBA/Biochemistry/media/MOPS_NoC_L-Cysteic_Acid.txt
PyFBA/Biochemistry/media/MOPS_NoC_L-Cysteine.txt
PyFBA/Biochemistry/media/MOPS_NoC_L-Fucose.txt
PyFBA/Biochemistry/media/MOPS_NoC_L-Glutamic_Acid.txt
PyFBA/Biochemistry/media/MOPS_NoC_L-Glutamine.txt
PyFBA/Biochemistry/media/MOPS_NoC_L-Isoleucine.txt
PyFBA/Biochemistry/media/MOPS_NoC_L-Leucine.txt
PyFBA/Biochemistry/media/MOPS_NoC_L-Lysine.txt
PyFBA/Biochemistry/media/MOPS_NoC_L-Methionine.txt
PyFBA/Biochemistry/media/MOPS_NoC_L-Phenylalanine.txt
PyFBA/Biochemistry/media/MOPS_NoC_L-Pyro-Glutamic_Acid.txt
PyFBA/Biochemistry/media/MOPS_NoC_L-Rhamnose.txt
PyFBA/Biochemistry/media/MOPS_NoC_L-Serine.txt
PyFBA/Biochemistry/media/MOPS_NoC_L-Sorbose.txt
PyFBA/Biochemistry/media/MOPS_NoC_L-Threonine.txt
PyFBA/Biochemistry/media/MOPS_NoC_L-Tryptophan.txt
PyFBA/Biochemistry/media/MOPS_NoC_L-Valine.txt
PyFBA/Biochemistry/media/MOPS_NoC_L-Xylose.txt
PyFBA/Biochemistry/media/MOPS_NoC_Lactic_Acid.txt
PyFBA/Biochemistry/media/MOPS_NoC_Lactulose.txt
PyFBA/Biochemistry/media/MOPS_NoC_Malic_Acid.txt
PyFBA/Biochemistry/media/MOPS_NoC_Melibiose.txt
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
PyFBA/Biochemistry/media/MOPS_NoC_Propionate.txt
PyFBA/Biochemistry/media/MOPS_NoC_Putrescine.txt
PyFBA/Biochemistry/media/MOPS_NoC_Pyruvate.txt
PyFBA/Biochemistry/media/MOPS_NoC_Quinate.txt
PyFBA/Biochemistry/media/MOPS_NoC_Raffinose.txt
PyFBA/Biochemistry/media/MOPS_NoC_Salicoside.txt
PyFBA/Biochemistry/media/MOPS_NoC_Succinate.txt
PyFBA/Biochemistry/media/MOPS_NoC_Sucrose.txt
PyFBA/Biochemistry/media/MOPS_NoC_Thymidine.txt
PyFBA/Biochemistry/media/MOPS_NoC_Trehalose.txt
PyFBA/Biochemistry/media/MOPS_NoC_Xylitol.txt
PyFBA/Biochemistry/media/MOPS_NoN_Adenine.txt
PyFBA/Biochemistry/media/MOPS_NoN_Adenosine.txt
PyFBA/Biochemistry/media/MOPS_NoN_Allantoin.txt
PyFBA/Biochemistry/media/MOPS_NoN_Beta-Phenylethylamine.txt
PyFBA/Biochemistry/media/MOPS_NoN_Biuret.txt
PyFBA/Biochemistry/media/MOPS_NoN_Cytidine.txt
PyFBA/Biochemistry/media/MOPS_NoN_Cytosine.txt
PyFBA/Biochemistry/media/MOPS_NoN_D-Methionine.txt
PyFBA/Biochemistry/media/MOPS_NoN_D-Valine.txt
PyFBA/Biochemistry/media/MOPS_NoN_Glycine.txt
PyFBA/Biochemistry/media/MOPS_NoN_Guanidine.txt
PyFBA/Biochemistry/media/MOPS_NoN_Histamine.txt
PyFBA/Biochemistry/media/MOPS_NoN_Inosine.txt
PyFBA/Biochemistry/media/MOPS_NoN_L-Arginine.txt
PyFBA/Biochemistry/media/MOPS_NoN_L-Glutathione.txt
PyFBA/Biochemistry/media/MOPS_NoN_L-Histidine.txt
PyFBA/Biochemistry/media/MOPS_NoN_L-Proline.txt
PyFBA/Biochemistry/media/MOPS_NoN_L-Pyro-Glutamic_Acid.txt
PyFBA/Biochemistry/media/MOPS_NoN_N-Acetyl-D-Glucosamine.txt
PyFBA/Biochemistry/media/MOPS_NoN_Negative_Control.txt
PyFBA/Biochemistry/media/MOPS_NoN_Thiourea.txt
PyFBA/Biochemistry/media/MOPS_NoN_Thymine.txt
PyFBA/Biochemistry/media/MOPS_NoN_Tyramine.txt
PyFBA/Biochemistry/media/MOPS_NoN_Uridine.txt
PyFBA/Biochemistry/media/__init__.py
PyFBA/cmd/__init__.py
PyFBA/cmd/assigned_functions_to_reactions.py
PyFBA/cmd/citation.py
PyFBA/cmd/entry.py
PyFBA/cmd/fba_from_reactions.py
PyFBA/cmd/fluxes.py
PyFBA/cmd/gapcreate.py
PyFBA/cmd/gapfill_from_reactions_multiple_conditions.py
PyFBA/cmd/gapfill_from_roles.py
PyFBA/cmd/media.py
PyFBA/cmd/reactions_to_roles.py
PyFBA/fba/__init__.py
PyFBA/fba/bounds.py
PyFBA/fba/create_stoichiometric_matrix.py
PyFBA/fba/external_reactions.py
PyFBA/fba/fluxes.py
PyFBA/fba/run_fba.py
PyFBA/filters/__init__.py
PyFBA/filters/reactions_and_proteins.py
PyFBA/filters/roles_and_complexes.py
PyFBA/filters/roles_and_reactions.py
PyFBA/gapfill/__init__.py
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
PyFBA/gapfill/subsystem.py
PyFBA/logs/__init__.py
PyFBA/logs/errors.py
PyFBA/logs/formatting.py
PyFBA/logs/messaging.py
PyFBA/lp/__init__.py
PyFBA/lp/glpk_solver.py
PyFBA/metabolism/__init__.py
PyFBA/metabolism/biomass.py
PyFBA/metabolism/compound.py
PyFBA/metabolism/enzyme.py
PyFBA/metabolism/reaction.py
PyFBA/model/__init__.py
PyFBA/model/build_model.py
PyFBA/model/fba.py
PyFBA/model/model.py
PyFBA/model_seed/__init__.py
PyFBA/model_seed/model_data.py
PyFBA/parse/SBML.py
PyFBA/parse/__init__.py
PyFBA/parse/config.py
PyFBA/parse/model_seed.py
PyFBA/parse/model_seed_solr.py
PyFBA/parse/rast.py
PyFBA/parse/read_media.py
PyFBA/tests/__init__.py
PyFBA/tests/assertDeepAlmostEqual.py
PyFBA/tests/reaction_list.txt
PyFBA/tests/roles.txt
PyFBA/tests/test_biomass_equation.py
PyFBA/tests/test_bisection.py
PyFBA/tests/test_bounds.py
PyFBA/tests/test_compound.py
PyFBA/tests/test_enzyme.py
PyFBA/tests/test_fba.py
PyFBA/tests/test_glpk_solver.py
PyFBA/tests/test_lp.py
PyFBA/tests/test_model_seed_object.py
PyFBA/tests/test_model_seed_parsing.py
PyFBA/tests/test_reaction.py
PyFBA/tests/test_reactions_and_roles.py
PyFBA/tests/test_read_media.py
PyFBA/tests/test_suggestions.py
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/reaction_info.py
example_code/reaction_statistics.py
example_code/run_fba_sbml.py
example_code/sbml_to_fba.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