├── .babelrc ├── .coveralls.yml ├── .gitignore ├── .ignore ├── .readthedocs.yml ├── .travis.yml ├── .vscode └── settings.json ├── CODE_OF_CONDUCT.md ├── CONTRIBUTING.md ├── DEPLOY.md ├── LICENSE ├── README.md ├── appveyor.yml ├── dev-server ├── index.html └── index.js ├── docs ├── Makefile ├── WEBSITE_MERGE ├── _static │ ├── EscherConverterGUI.png │ ├── Preferences.png │ ├── bar.png │ ├── console.png │ ├── custom.css │ ├── data_menu.png │ ├── edit_menu.png │ ├── escher-logo_256.png │ ├── escherconverter_io.png │ ├── example_data │ │ ├── S3_iJO1366_anaerobic_FBA_flux.json │ │ ├── S4_McCloskey2013_aerobic_metabolomics.csv │ │ ├── S5_iJO1366.Glycolysis_PPP_AA_Nucleotides.json │ │ ├── S6_RNA-seq_aerobic_to_anaerobic.csv │ │ ├── aerobic_anaerobic_E_coli_RNA-seq.json │ │ ├── aerobic_anaerobic_E_coli_RNA-seq_negatives.json │ │ ├── gene_data_iJO1366.json │ │ ├── gene_data_names_iJO1366.json │ │ ├── iJO1366.json │ │ ├── make_data.py │ │ ├── metabolite_data_diff_iJO1366.json │ │ ├── metabolite_data_iJO1366.json │ │ ├── metabolite_data_names_iJO1366.json │ │ ├── reaction_data_diff_iJO1366.json │ │ ├── reaction_data_iJO1366.json │ │ └── reaction_data_names_iJO1366.json │ ├── hover.png │ ├── iJO1366.png │ ├── jar_icon.png │ ├── launch_page.png │ ├── lgplv3-147x51.png │ ├── map_menu.png │ ├── menu.png │ ├── model_menu.png │ ├── reaction_data_with_nd.png │ ├── reaction_settings.png │ ├── screen1.png │ ├── settings.png │ ├── tooltip_bar.png │ ├── tooltip_count.png │ ├── tooltip_image.png │ └── view_menu.png ├── _templates │ └── layout.html ├── build_docs ├── conf.py ├── convert_maps.rst ├── developer-tutorial.rst ├── development.rst ├── escher-python.ipynb ├── escher_and_cobrapy.rst ├── escherconverter.rst ├── getting_started.rst ├── index.rst ├── javascript_api.rst ├── license.rst ├── make.bat ├── python_api.rst └── tips-and-tricks.rst ├── icons ├── LICENSE.txt ├── README.txt ├── config.json ├── css │ └── fontello.css └── font │ ├── fontello.eot │ ├── fontello.svg │ ├── fontello.ttf │ ├── fontello.woff │ └── fontello.woff2 ├── jsonschema └── 1-0-0 ├── jupyter ├── lab-extension.js └── notebook-extension.js ├── package.json ├── postBuild ├── py ├── MANIFEST.in ├── escher.json ├── escher │ ├── __init__.py │ ├── plots.py │ ├── static │ │ ├── escher.min.js │ │ ├── escher.min.js.map │ │ ├── extension.js │ │ ├── jsonschema │ │ │ └── 1-0-0 │ │ └── package.json │ ├── templates │ │ └── standalone.html │ ├── testing_data │ │ ├── iJO1366.json │ │ ├── metabolite_data_iJO1366.json │ │ └── reaction_data_iJO1366.json │ ├── tests │ │ ├── example.json │ │ ├── test_plots.py │ │ ├── test_urls.py │ │ ├── test_utils.py │ │ └── test_validate.py │ ├── urls.py │ ├── util.py │ ├── validate.py │ └── version.py ├── pytest.ini └── setup.py ├── src ├── Behavior.js ├── Brush.js ├── BuildInput.js ├── Builder-embed.css ├── Builder.css ├── Builder.jsx ├── ButtonPanel.css ├── ButtonPanel.jsx ├── CallbackManager.js ├── Canvas.js ├── CobraModel.js ├── DataMenu.js ├── 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