├── .github ├── dependabot.yml └── workflows │ └── build.yml ├── .gitignore ├── LICENSE ├── MANIFEST.in ├── README.md ├── RELEASE.md ├── binder ├── atom_rules.ipynb ├── conftest.py ├── data │ ├── EC-RP_IMS-RP_IC-RP_data_for_models.csv │ ├── calibrated_6572pars.npy │ ├── enzymatic_exp_sd.npy │ └── enzymatic_product_data.npy ├── earm_correction.ipynb ├── environment.yml ├── fig2_multiresolution_earm.ipynb ├── fig3_dynamic_earm.ipynb ├── tellurium_example.ipynb └── visualizing_model_components.ipynb ├── docs ├── Makefile ├── conf.py ├── conftest.py ├── environment.yml ├── graph_formats_example.ipynb ├── graphs_formats │ ├── activated_stat1alpha_induction_of_the_irf1_gene.xml │ ├── bid_network.sif │ ├── earm.json │ ├── gexf_network.gexf │ ├── graphml_example2.graphml │ ├── karate.gml │ └── yaml_network.yaml ├── index.rst ├── installation.rst ├── make.bat ├── modules │ ├── index.rst │ ├── networkx_viz.rst │ ├── pysb_viz.rst │ └── tellurium_viz.rst ├── pysb_tutorial.ipynb ├── pytest-sanitize.ini └── tellurium_examples.ipynb ├── double_enzymatic_species.png ├── earm_communities.png ├── graphml.png ├── js ├── README.md ├── lib │ ├── cytoscape.css │ ├── cytoscape.js │ ├── elements_style.css │ ├── embed.js │ ├── extension.js │ ├── index.js │ ├── labplugin.js │ └── sif.js ├── package-lock.json ├── package.json └── webpack.config.js ├── meta.yaml ├── pyvipr.json ├── pyvipr ├── __init__.py ├── _version.py ├── bipartite_projection.py ├── examples_models │ ├── __init__.py │ ├── albeck_modules.py │ ├── bid_compartments.py │ ├── double_enzymatic_sbml.xml │ ├── earm_incorrect.py │ ├── ensemble_1_bng │ │ ├── ensemble_1.bngl │ │ └── ensemble_1_opts.txt │ ├── lopez_embedded.py │ ├── lopez_modules.py │ ├── mm_two_paths_model.py │ ├── organelle_transport.bngl │ ├── organelle_transport.py │ └── shared.py ├── model_simresult_to_json.py ├── network_viz │ ├── __init__.py │ ├── network_viz.py │ └── views.py ├── pysb_viz │ ├── __init__.py │ ├── dynamic_viz.py │ ├── static_viz.py │ └── views.py ├── staticlab │ ├── README.md │ ├── package.json │ └── static │ │ ├── 142.46114563434fa17e1341.js │ │ ├── 142.d1260c428e39ebae8def.js │ │ ├── 143.f11a2433740b8bbe55e6.js │ │ ├── 172.fb9e62364992e8ef2ad9.js │ │ ├── 187.9f64e19bfaa3de00cd17.js │ │ ├── 261.a9f0fda99f6915756664.js │ │ ├── 486.c9ecbbde2292967a2e67.js │ │ ├── 486.c9ecbbde2292967a2e67.js.LICENSE.txt │ │ ├── 504.2f138964464ec46cabfa.js │ │ ├── 526.541decf99aa6961a98b5.js │ │ ├── 526.541decf99aa6961a98b5.js.LICENSE.txt │ │ ├── 548.c8a9f5e70fc39dff5c0b.js │ │ ├── 568.9c1804903f6b5697e24b.js │ │ ├── 568.e509d56a970619cb6312.js │ │ ├── 578.4110b3ecea709bc7a495.js │ │ ├── 58.5c474e2176e381f75172.js │ │ ├── 58.5c474e2176e381f75172.js.LICENSE.txt │ │ ├── 607.a83ab1a720369d8fc52d.js │ │ ├── 703.ec27aa23911b43f4c52e.js │ │ ├── 713.edae77d19a3788603cd4.js │ │ ├── 724.3fbb55fa396222ea2da8.js │ │ ├── 724.3fbb55fa396222ea2da8.js.LICENSE.txt │ │ ├── 73.4ee7163aeaafcb23435a.js │ │ ├── 755.46877ba82c346b195aac.js │ │ ├── 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