├── .gitignore ├── .vscode └── launch.json ├── LICENSE ├── README.md ├── backend ├── README.md ├── docker-compose.yml ├── elastic │ ├── Dockerfile │ ├── config │ │ └── elasticsearch.yml │ └── es_backup.tar.gz ├── gene-ontology │ ├── Dockerfile │ ├── app.py │ ├── go.py │ └── requirements.txt ├── predictor │ ├── Dockerfile │ ├── dc.proto │ ├── dc │ │ └── dc.pb.go │ ├── dc_pb2.py │ ├── dc_pb2_grpc.py │ └── main.go ├── props │ ├── Dockerfile │ └── app.go ├── search-proxy │ ├── Dockerfile │ ├── app.js │ ├── bin │ │ └── www │ ├── package-lock.json │ ├── package.json │ ├── public │ │ └── stylesheets │ │ │ └── style.css │ ├── routes │ │ ├── index.js │ │ ├── map.js │ │ └── search.js │ └── views │ │ ├── error.jade │ │ ├── index.jade │ │ └── layout.jade └── webserver │ ├── Dockerfile │ ├── dc.conf │ └── static │ ├── app │ ├── bundle.js │ ├── index.html │ └── vendor.bundle.js │ ├── images │ └── title-final.svg │ ├── index.html │ └── style.css ├── data-builder ├── .gitignore ├── DAG_test.ipynb ├── Full-go-tree-builder_from_cyjs.ipynb ├── Full-go-tree_generator.ipynb ├── Full-go-updater.ipynb ├── Tweak_GO_Tree.ipynb ├── annotate_result.ipynb ├── annotation_columns.txt ├── cols.txt ├── costanzo_2016_genes ├── data │ └── README.md ├── elasticsearch_idex_generator.ipynb ├── goID_2_name.tab ├── mock_subnetwork.ipynb ├── p_cols.txt ├── path_finder_test.ipynb ├── phenotype_cols.txt ├── sample-simulation │ ├── subnet-d3.json │ ├── testNetwork.txt │ ├── testNetwork_style.txt │ └── tree1.html ├── tree_generator-clixo-final.ipynb ├── tree_generator.ipynb ├── update_clixo.ipynb ├── yeast_clean4.txt └── yeastnet_raw_interactions.ipynb ├── docs └── images │ ├── 1.2-example-search.png │ ├── 1.2-overview.png │ ├── 1.2-result.png │ ├── 1.2-searchpanel.png │ ├── 1.2-subsystem-search.png │ ├── 1.4_overview.PNG │ ├── full-result.png │ ├── gene-search.png │ ├── go-details.png │ ├── locate-term.png │ ├── locate1.png │ ├── neural-network-view.png │ ├── neuron-expanded.png │ ├── overview-annotated.png │ ├── overview.png │ ├── raw-interactions.png │ └── result-view.png ├── frontend ├── .babelrc ├── .eslintrc.yml ├── .gitignore ├── Dockerfile ├── LICENSE ├── Readme.md ├── client │ ├── actions │ │ ├── commands.js │ │ ├── cyjs.js │ │ ├── message.js │ │ ├── network.js │ │ ├── ontologies.js │ │ ├── property.js │ │ ├── query-genes.js │ │ ├── search.js │ │ └── ui-state.js │ ├── assets │ │ ├── config.json │ │ ├── images │ │ │ ├── cytoscape-logo-orange.svg │ │ │ ├── cytoscape-logo-white.svg │ │ │ ├── github-white.svg │ │ │ └── github.svg │ │ └── preset-styles.json │ ├── components │ │ ├── ClosableAppBar │ │ │ ├── index.jsx │ │ │ └── style.css │ │ ├── Commands │ │ │ ├── index.js │ │ │ └── style.css │ │ ├── ErrorDialog │ │ │ └── index.jsx │ │ ├── Loading │ │ │ ├── index.js │ │ │ └── style.css │ │ ├── MainMenu │ │ │ ├── index.js │ │ │ └── style.css │ │ ├── MessagePanel │ │ │ └── index.jsx │ │ ├── NetworkPanel │ │ │ ├── VisualStyle.js │ │ │ ├── index.jsx │ │ │ ├── style.css │ │ │ └── worker.js │ │ ├── NetworkSelector │ │ │ └── index.jsx │ │ ├── NetworkViewer │ │ │ ├── index.jsx │ │ │ └── style.css │ │ ├── PropertyPanel │ │ │ ├── ClixoDetails.jsx │ │ │ ├── FilterPanel.jsx │ │ │ ├── GeneList.jsx │ │ │ ├── GoDetails.jsx │ │ │ ├── RawInteractionPanel.jsx │ │ │ ├── SubNetworkView.jsx │ │ │ ├── TitleBar.jsx │ │ │ ├── TreeView.jsx │ │ │ └── index.jsx │ │ ├── RunningOverlay │ │ │ └── index.jsx │ │ ├── SearchPanel │ │ │ ├── ExampleQueries.jsx │ │ │ ├── ExampleTermSearch.jsx │ │ │ ├── GeneList.jsx │ │ │ ├── GenotypePanel.jsx │ │ │ ├── ListTab.jsx │ │ │ ├── SearchTab.jsx │ │ │ ├── SimulationTypeSelector.jsx │ │ │ ├── StructureSelectorPanel.jsx │ │ │ ├── TermSearchPanel.jsx │ │ │ ├── gene-list.js │ │ │ ├── index.jsx │ │ │ └── style.css │ │ ├── Speedometer │ │ │ ├── MinimalGauge.jsx │ │ │ └── index.jsx │ │ ├── StyleSelector │ │ │ └── index.js │ │ ├── SubTreePanel │ │ │ ├── AnimatedArrow.jsx │ │ │ ├── DefaultPanel.jsx │ │ │ ├── LegendColor.jsx │ │ │ ├── LegendLine.jsx │ │ │ ├── default.svg │ │ │ ├── index.jsx │ │ │ └── style.css │ │ ├── TopPage │ │ │ ├── Footer.js │ │ │ ├── Title.js │ │ │ ├── index.js │ │ │ └── style.css │ │ └── TreeTitleBar │ │ │ └── index.jsx │ ├── containers │ │ ├── Entrance │ │ │ ├── index.js │ │ │ └── style.css │ │ └── NetworkView │ │ │ ├── index.jsx │ │ │ └── style.css │ ├── index.html │ ├── index.js │ ├── middleware │ │ ├── data-fetch.js │ │ ├── index.js │ │ └── logger.js │ ├── reducers │ │ ├── commands.js │ │ ├── config.js │ │ ├── currentnetwork.js │ │ ├── currentvs.js │ │ ├── cy-events.js │ │ ├── cycommands.js │ │ ├── datasource.js │ │ ├── index.js │ │ ├── message.js │ │ ├── network.js │ │ ├── ontologies.js │ │ ├── property.js │ │ ├── query-genes.js │ │ ├── search.js │ │ ├── ui-state.js │ │ └── visualstyles.js │ └── store │ │ └── index.js ├── nginx.conf ├── package-lock.json ├── package.json └── webpack.config.js └── training ├── Topology ├── GO:0000790_topology └── GO:0006281_topology ├── TrainData ├── GO:0000790_testing_data_2016_0 ├── 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