├── .gitignore ├── .vscode └── settings.json ├── Dockerfile ├── LICENSE ├── README.md ├── docs ├── conf.py ├── drugtarget.rst ├── howtouse.rst ├── images │ ├── appmanagerKEGGscape.png │ ├── appstore.png │ ├── batchimport.PNG │ ├── bundlemenu.png │ ├── downloadKGML.png │ ├── download_seedmodel.png │ ├── drugtarget_table.png │ ├── ecoliTCA.png │ ├── edgeBandledNetwork.png │ ├── export_table_csv.png │ ├── export_table_pulldown.png │ ├── get_all_eco_kgmls.png │ ├── highlight_drugtarget.png │ ├── icon2select2open.png │ ├── import.png │ ├── import_drugtarget.png │ ├── install.png │ ├── kegg_model_genediff.png │ ├── swagger1.PNG │ ├── swagger2.PNG │ ├── table_export_from_menu.png │ └── tcacycle.png ├── index.rst ├── install.rst ├── mergemodel.rst └── pythonscripting.rst ├── pom.xml ├── src ├── main │ ├── java │ │ └── org │ │ │ └── cytoscape │ │ │ └── keggscape │ │ │ └── internal │ │ │ ├── CyActivator.java │ │ │ ├── KeggscapeDocumentation.java │ │ │ ├── read │ │ │ └── kgml │ │ │ │ ├── AbstractReaderFactory.java │ │ │ │ ├── KEGGTags.java │ │ │ │ ├── KGMLMapper.java │ │ │ │ ├── KeggConstants.java │ │ │ │ ├── KeggscapeFileFilter.java │ │ │ │ ├── KeggscapeNetworkReader.java │ │ │ │ └── KeggscapeNetworkReaderFactory.java │ │ │ ├── rest │ │ │ ├── HeadlessTaskMonitor.java │ │ │ ├── KeggImportParams.java │ │ │ ├── KeggscapeImportResult.java │ │ │ └── KeggscapeResource.java │ │ │ ├── style │ │ │ └── KGMLVisualStyleBuilder.java │ │ │ ├── task │ │ │ ├── ExpandPathwayContextMenuTaskFactory.java │ │ │ ├── ExpandPathwayTask.java │ │ │ ├── ImportKGMLTask.java │ │ │ ├── MapExtraDataTask.java │ │ │ ├── MapExtraDataTaskFactory.java │ │ │ ├── OpenDetailsInBrowserTask.java │ │ │ ├── OpenDetailsInBrowserTaskFactory.java │ │ │ └── UpdateStyleTask.java │ │ │ ├── ui │ │ │ ├── PathwaySelectorDialog.java │ │ │ └── ShowPathwaySelectorAction.java │ │ │ └── wsclient │ │ │ ├── TogowsClient.java │ │ │ └── TogowsTags.java │ └── resources │ │ ├── KGML_v0.7.2_.dtd │ │ ├── compoundNames.txt │ │ ├── docs │ │ └── images │ │ │ ├── global_human.png │ │ │ ├── link_to_compound.png │ │ │ ├── link_to_kgml.png │ │ │ ├── link_to_pathway.png │ │ │ ├── nested_pathway.png │ │ │ └── tca.png │ │ ├── getCpdNames.py │ │ ├── images │ │ ├── global_human.png │ │ ├── global_human_500px.png │ │ ├── importMaplinkPathway.png │ │ ├── kgml2.png │ │ └── turnOffTogoWS.png │ │ └── plugin.props └── test │ ├── java │ └── org │ │ └── cytoscape │ │ └── data │ │ └── reader │ │ └── kgml │ │ └── test │ │ ├── AbstractKeggReaderTest.java │ │ ├── DiseasePathwayTest.java │ │ ├── KEGGClientTest.java │ │ ├── ReadMetabolicPathwayTest.java │ │ └── SimpleClientTest.java │ └── resources │ └── testData │ ├── bsu00010.cys │ ├── bsu01100.cys │ ├── entry_table │ ├── kgml │ ├── metabolic │ │ ├── ec │ │ │ ├── ec00010.xml │ │ │ ├── ec00020.xml │ │ │ ├── ec00030.xml │ │ │ ├── ec00290.xml │ │ │ ├── ec00340.xml │ │ │ ├── ec01100.xml │ │ │ └── ec01110.xml │ │ ├── ko │ │ │ ├── ko00010.xml │ │ │ ├── ko00020.xml │ │ │ ├── ko00030.xml │ │ │ ├── ko00290.xml │ │ │ ├── ko00340.xml │ │ │ ├── ko01100.xml │ │ │ └── ko01110.xml │ │ └── organisms │ │ │ ├── bsu │ │ │ ├── bsu00010.xml │ │ │ ├── bsu00020.xml │ │ │ ├── bsu00030.xml │ │ │ ├── bsu00290.xml │ │ │ ├── bsu00340.xml │ │ │ ├── bsu01100.xml │ │ │ └── bsu01110.xml │ │ │ ├── eco │ │ │ ├── eco00010.xml │ │ │ ├── eco00020.xml │ │ │ ├── eco00030.xml │ │ │ ├── eco00290.xml │ │ │ ├── eco00340.xml │ │ │ ├── eco01100.xml │ │ │ └── eco01110.xml │ │ │ ├── hsa │ │ │ ├── hsa00010.xml │ │ │ ├── hsa00020.xml │ │ │ ├── hsa00030.xml │ │ │ ├── hsa00290.xml │ │ │ ├── hsa00340.xml │ │ │ └── hsa01100.xml │ │ │ └── sce │ │ │ ├── sce00010.xml │ │ │ ├── sce00020.xml │ │ │ ├── sce00030.xml │ │ │ ├── sce00290.xml │ │ │ ├── sce00340.xml │ │ │ ├── sce01100.xml │ │ │ └── sce01110.xml │ └── non-metabolic │ │ └── organisms │ │ ├── bsu │ │ ├── bsu02010.xml │ │ ├── bsu02020.xml │ │ ├── bsu02030.xml │ │ ├── bsu02040.xml │ │ ├── bsu02060.xml │ │ ├── bsu03010.xml │ │ ├── bsu03018.xml │ │ ├── bsu03020.xml │ │ ├── bsu03030.xml │ │ ├── bsu03060.xml │ │ ├── bsu03070.xml │ │ ├── bsu03410.xml │ │ ├── bsu03420.xml │ │ ├── bsu03430.xml │ │ ├── bsu03440.xml │ │ └── bsu03450.xml │ │ └── hsa │ │ ├── hsa03030.xml │ │ ├── hsa04060.xml │ │ ├── hsa05010.xml │ │ └── hsa05200.xml │ └── sampleTCA.attr ├── usecase ├── CytoscapeREST_KEGG_time_series.ipynb ├── f1000-cyauto-workflow.Rmd └── figures │ ├── fig1.png │ ├── fig2.png │ └── keggscape-in-appmanager.PNG └── wiki ├── data ├── README.md ├── light-20.csv ├── light-4.csv ├── light-dark-20.csv └── light-dark-4.csv └── images ├── appmanager.png ├── cell4enhancedgraphics.png ├── create-column4enhancedgraphics.png ├── import-metabolome.png ├── import-ttest.png ├── intro-example.png ├── kgmldownloadlink.png ├── merge-metabolome.png ├── merge-setting.png ├── metabolome-visualization.png ├── quickstart.png ├── vizmap-enhancedgraphics.png └── vizmap-setting.png /.gitignore: -------------------------------------------------------------------------------- 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