.gitignore
LICENSE
MANIFEST.in
README.md
RELEASE.md
double_enzymatic_species.png
earm_communities.png
graphml.png
meta.yaml
pyvipr.json
pyvipr_dynamic.gif
pyvipr_logo.png
readthedocs.yml
setup.cfg
setup.py
tellurium_example.png
.github/dependabot.yml
.github/workflows/build.yml
binder/atom_rules.ipynb
binder/conftest.py
binder/earm_correction.ipynb
binder/environment.yml
binder/fig2_multiresolution_earm.ipynb
binder/fig3_dynamic_earm.ipynb
binder/tellurium_example.ipynb
binder/visualizing_model_components.ipynb
binder/data/EC-RP_IMS-RP_IC-RP_data_for_models.csv
binder/data/calibrated_6572pars.npy
binder/data/enzymatic_exp_sd.npy
binder/data/enzymatic_product_data.npy
docs/Makefile
docs/conf.py
docs/conftest.py
docs/environment.yml
docs/graph_formats_example.ipynb
docs/index.rst
docs/installation.rst
docs/make.bat
docs/pysb_tutorial.ipynb
docs/pytest-sanitize.ini
docs/tellurium_examples.ipynb
docs/graphs_formats/activated_stat1alpha_induction_of_the_irf1_gene.xml
docs/graphs_formats/bid_network.sif
docs/graphs_formats/earm.json
docs/graphs_formats/gexf_network.gexf
docs/graphs_formats/graphml_example2.graphml
docs/graphs_formats/karate.gml
docs/graphs_formats/yaml_network.yaml
docs/modules/index.rst
docs/modules/networkx_viz.rst
docs/modules/pysb_viz.rst
docs/modules/tellurium_viz.rst
js/README.md
js/package-lock.json
js/package.json
js/webpack.config.js
js/lib/cytoscape.css
js/lib/cytoscape.js
js/lib/elements_style.css
js/lib/embed.js
js/lib/extension.js
js/lib/index.js
js/lib/labplugin.js
js/lib/sif.js
pyvipr/__init__.py
pyvipr/_version.py
pyvipr/bipartite_projection.py
pyvipr/model_simresult_to_json.py
pyvipr/util.py
pyvipr/util_networkx.py
pyvipr/viz.py
pyvipr.egg-info/PKG-INFO
pyvipr.egg-info/SOURCES.txt
pyvipr.egg-info/dependency_links.txt
pyvipr.egg-info/not-zip-safe
pyvipr.egg-info/requires.txt
pyvipr.egg-info/top_level.txt
pyvipr/examples_models/__init__.py
pyvipr/examples_models/albeck_modules.py
pyvipr/examples_models/bid_compartments.py
pyvipr/examples_models/double_enzymatic_sbml.xml
pyvipr/examples_models/earm_incorrect.py
pyvipr/examples_models/lopez_embedded.py
pyvipr/examples_models/lopez_modules.py
pyvipr/examples_models/mm_two_paths_model.py
pyvipr/examples_models/organelle_transport.bngl
pyvipr/examples_models/organelle_transport.py
pyvipr/examples_models/shared.py
pyvipr/examples_models/ensemble_1_bng/ensemble_1.bngl
pyvipr/examples_models/ensemble_1_bng/ensemble_1_opts.txt
pyvipr/network_viz/__init__.py
pyvipr/network_viz/network_viz.py
pyvipr/network_viz/views.py
pyvipr/pysb_viz/__init__.py
pyvipr/pysb_viz/dynamic_viz.py
pyvipr/pysb_viz/static_viz.py
pyvipr/pysb_viz/views.py
pyvipr/static/extension.js
pyvipr/static/index.js
pyvipr/static/index.js.LICENSE.txt
pyvipr/static/index.js.map
pyvipr/staticlab/README.md
pyvipr/staticlab/package.json
pyvipr/tellurium_viz/__init__.py
pyvipr/tellurium_viz/dynamic_viz.py
pyvipr/tellurium_viz/static_viz.py
pyvipr/tellurium_viz/views.py
pyvipr/tests/test_pysb_static.py