LICENSE
MANIFEST.in
README.rst
requirements.txt
setup.cfg
setup.py
versioneer.py
cameo/__init__.py
cameo/_version.py
cameo/config.py
cameo/exceptions.py
cameo/io.py
cameo/parallel.py
cameo/util.py
cameo.egg-info/PKG-INFO
cameo.egg-info/SOURCES.txt
cameo.egg-info/dependency_links.txt
cameo.egg-info/entry_points.txt
cameo.egg-info/requires.txt
cameo.egg-info/top_level.txt
cameo/api/__init__.py
cameo/api/designer.py
cameo/api/hosts.py
cameo/api/products.py
cameo/core/__init__.py
cameo/core/manipulation.py
cameo/core/model_dual.py
cameo/core/pathway.py
cameo/core/result.py
cameo/core/strain_design.py
cameo/core/target.py
cameo/core/utils.py
cameo/data/__init__.py
cameo/data/metanetx.json.gz
cameo/data/metanetx.py
cameo/data/metanetx_chem_prop.json.gz
cameo/flux_analysis/__init__.py
cameo/flux_analysis/analysis.py
cameo/flux_analysis/simulation.py
cameo/flux_analysis/structural.py
cameo/flux_analysis/util.py
cameo/models/__init__.py
cameo/models/universal.py
cameo/models/webmodels.py
cameo/models/json/e_coli_core.json
cameo/models/json/iJO1366.json
cameo/models/json/iMM904.json
cameo/models/sbml/iJO1366.xml
cameo/models/sbml/iMM904.xml
cameo/models/sbml/legacy_sbml/iJO1366.xml
cameo/models/sbml/legacy_sbml/iMM904.xml
cameo/models/universal_models/metanetx_universal_model_bigg.json
cameo/models/universal_models/metanetx_universal_model_bigg_rhea.json
cameo/models/universal_models/metanetx_universal_model_bigg_rhea_kegg.json
cameo/models/universal_models/metanetx_universal_model_bigg_rhea_kegg_brenda.json
cameo/models/universal_models/metanetx_universal_model_rhea.json
cameo/network_analysis/__init__.py
cameo/network_analysis/networkx_based.py
cameo/network_analysis/util.py
cameo/strain_design/__init__.py
cameo/strain_design/deterministic/__init__.py
cameo/strain_design/deterministic/flux_variability_based.py
cameo/strain_design/deterministic/linear_programming.py
cameo/strain_design/heuristic/__init__.py
cameo/strain_design/heuristic/evolutionary_based.py
cameo/strain_design/heuristic/evolutionary/__init__.py
cameo/strain_design/heuristic/evolutionary/archives.py
cameo/strain_design/heuristic/evolutionary/decoders.py
cameo/strain_design/heuristic/evolutionary/evaluators.py
cameo/strain_design/heuristic/evolutionary/generators.py
cameo/strain_design/heuristic/evolutionary/genomes.py
cameo/strain_design/heuristic/evolutionary/metrics.py
cameo/strain_design/heuristic/evolutionary/objective_functions.py
cameo/strain_design/heuristic/evolutionary/observers.py
cameo/strain_design/heuristic/evolutionary/optimization.py
cameo/strain_design/heuristic/evolutionary/plotters.py
cameo/strain_design/heuristic/evolutionary/processing.py
cameo/strain_design/heuristic/evolutionary/stats.py
cameo/strain_design/heuristic/evolutionary/variators.py
cameo/strain_design/heuristic/evolutionary/multiprocess/__init__.py
cameo/strain_design/heuristic/evolutionary/multiprocess/migrators.py
cameo/strain_design/heuristic/evolutionary/multiprocess/observers.py
cameo/strain_design/heuristic/evolutionary/multiprocess/optimization.py
cameo/strain_design/heuristic/evolutionary/multiprocess/plotters.py
cameo/strain_design/pathway_prediction/__init__.py
cameo/strain_design/pathway_prediction/pathway_predictor.py
cameo/strain_design/pathway_prediction/util.py
cameo/ui/__init__.py
cameo/ui/assets/loading_wave.gif
cameo/ui/assets/searching.gif
cameo/visualization/__init__.py
cameo/visualization/escher_ext.py
cameo/visualization/palette.py
cameo/visualization/sympy_ext.py
cameo/visualization/visualization.py
cameo/visualization/plotting/__init__.py
cameo/visualization/plotting/abstract.py
cameo/visualization/plotting/with_bokeh.py
cameo/visualization/plotting/with_ggplot.py
cameo/visualization/plotting/with_plotly.py
cli/__init__.py
cli/cli.py
tests/__init__.py
tests/conftest.py
tests/test_api.py
tests/test_core_strain_design.py
tests/test_flux_analysis.py
tests/test_io.py
tests/test_network_analysis.py
tests/test_parallel.py
tests/test_pathway_predictions.py
tests/test_solver_based_model.py
tests/test_strain_design_deterministic.py
tests/test_strain_design_heuristics.py
tests/test_targets.py
tests/test_util.py
tests/test_webmodels.py
tests/data/EcoliCore.xml
tests/data/REFERENCE_DiffFVA1.csv
tests/data/REFERENCE_DiffFVA2.csv
tests/data/REFERENCE_PPP_o2_EcoliCore.csv
tests/data/REFERENCE_PPP_o2_EcoliCore_ac.csv
tests/data/REFERENCE_PPP_o2_glc_EcoliCore.csv
tests/data/REFERENCE_flux_ranges_EcoliCore.csv
tests/data/ecoli_core_model.xml
tests/data/fix_size_candidates.pkl
tests/data/iAF1260.xml
tests/data/iJO1366.pickle
tests/data/iJO1366.xml
tests/data/iMM904.xml
tests/data/iTO977_v1.01_cobra.xml
tests/data/make_data_sets.py
tests/data/salmonella.pickle
tests/data/toy_model_Papin_2003.xml
tests/data/update-pickles.py
tests/data/variable_size_candidates.pkl
tests/data/legacy_models/EcoliCore.xml
tests/data/legacy_models/REFERENCE_DiffFVA1.pickle
tests/data/legacy_models/REFERENCE_DiffFVA2.pickle
tests/data/legacy_models/REFERENCE_flux_ranges_EcoliCore.csv
tests/data/legacy_models/ecoli_core_model.xml
tests/data/legacy_models/iAF1260.xml
tests/data/legacy_models/iJO1366.xml
tests/data/legacy_models/iMM904.xml
tests/data/legacy_models/iTO977_v1.01_cobra.xml
tests/data/legacy_models/toy_model_Papin_2003.xml