├── .gitattributes ├── .github ├── ISSUE_TEMPLATE │ ├── bug_report.md │ └── feature_request.md └── workflows │ └── python-publish.yml ├── .gitignore ├── .travis.yml ├── CHANGELOG.md ├── LICENSE.txt ├── README.rst ├── docs_gen ├── Makefile ├── docs_gen.sh ├── requirements.txt └── source │ ├── .ipynb_checkpoints │ └── quickstart-checkpoint.ipynb │ ├── cobamp.algorithms.rst │ ├── cobamp.analysis.rst │ ├── cobamp.core.rst │ ├── cobamp.nullspace.rst │ ├── cobamp.rst │ ├── cobamp.utilities.rst │ ├── cobamp.wrappers.rst │ ├── conf.py │ ├── index.rst │ ├── installation.rst │ ├── modules.rst │ ├── quickstart.ipynb │ └── requirements.txt ├── examples ├── GBconsensus_resources │ └── gb_plots.py ├── ecoli_core_model.py ├── gbconsensus.py ├── gbconsensus_model_compression.py ├── iAF1260_resources │ ├── iAF1260_comp_bound_map.txt │ ├── iAF1260_comp_exclusions.txt │ ├── iAF1260_comp_metnames.txt │ ├── iAF1260_comp_orx_map.txt │ ├── iAF1260_comp_rxnames.txt │ ├── iAF1260_comp_stoich.csv │ └── iAF1260_comp_synthlethals.txt └── iaf1260.py ├── notice.txt ├── requirements.txt ├── setup.py ├── src └── cobamp │ ├── __init__.py │ ├── algorithms │ ├── __init__.py │ └── kshortest.py │ ├── analysis │ ├── __init__.py │ ├── frequency.py │ ├── graph.py │ └── plotting.py │ ├── core │ ├── __init__.py │ ├── cb_analysis.py │ ├── linear_systems.py │ ├── models.py │ ├── optimization.py │ └── transformer.py │ ├── gpr │ ├── __init__.py │ ├── core.py │ └── integration.py │ ├── nullspace │ ├── __init__.py │ ├── nullspace.py │ └── subset_reduction.py │ ├── utilities │ ├── __init__.py │ ├── context.py │ ├── file_io.py │ ├── hash.py │ ├── linear_system_diagnostics.py │ ├── parallel.py │ ├── postfix_expressions.py │ ├── printing.py │ ├── property_management.py │ ├── set.py │ ├── test.py │ └── tree.py │ └── wrappers │ ├── __init__.py │ ├── cobamp.py │ ├── cobra.py │ ├── core.py │ ├── external_wrappers.py │ ├── framed.py │ └── method_wrappers.py └── tests ├── ecoli_compression_test.py ├── linear_system_optimizer_test.py ├── parallel_simulation_test.py ├── property_dictionary_test.py ├── resources ├── toy_efm_mcs.png └── toy_network.png ├── test_gmcs_toy.py ├── toy_model_test.py └── toy_model_test_with_api.py /.gitattributes: -------------------------------------------------------------------------------- 1 | docs_gen/* linguist-generated=true 2 | -------------------------------------------------------------------------------- /.github/ISSUE_TEMPLATE/bug_report.md: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/BioSystemsUM/cobamp/HEAD/.github/ISSUE_TEMPLATE/bug_report.md -------------------------------------------------------------------------------- /.github/ISSUE_TEMPLATE/feature_request.md: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/BioSystemsUM/cobamp/HEAD/.github/ISSUE_TEMPLATE/feature_request.md 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