Update Readme.md, Analysis/EUvsVirus/Covid19KG_Fraunhofer_Hipathia/.gitkeep,...

Update Readme.md, Analysis/EUvsVirus/Covid19KG_Fraunhofer_Hipathia/.gitkeep, Analysis/EUvsVirus/GMLs_AF__four_maps/.gitkeep, Analysis/EUvsVirus/GMLs_AF__four_maps/Apoptosis.gml, Analysis/EUvsVirus/GMLs_AF__four_maps/Apoptosis_AF.pdf, Analysis/EUvsVirus/GMLs_AF__four_maps/ER-stress.gml, Analysis/EUvsVirus/GMLs_AF__four_maps/ER-stress_AF.pdf, Analysis/EUvsVirus/GMLs_AF__four_maps/Interferon.gml, Analysis/EUvsVirus/GMLs_AF__four_maps/Interferon_AF.pdf, Analysis/EUvsVirus/GMLs_AF__four_maps/PAMP.graphml, Analysis/EUvsVirus/GMLs_AF__four_maps/PAMP_AF.pdf, Analysis/EUvsVirus/Hipathia_maps/.gitkeep, Analysis/EUvsVirus/Hipathia_operableMaps/.gitkeep, Analysis/EUvsVirus/Hipathia_operableMaps/hsaCovid19KG.att, Analysis/EUvsVirus/Hipathia_operableMaps/hsaCovid19KG.sif, Analysis/EUvsVirus/MINERVA-API/drug_targets/ACE2-Spike-drugs.txt, Analysis/EUvsVirus/MINERVA-API/drug_targets/Apoptosis.txt, Analysis/EUvsVirus/MINERVA-API/drug_targets/ER stress.txt, 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Analysis/EUvsVirus/MINERVA-API/element_jsons/HCoVs autophagy (WP4863)_annotations.json, Analysis/EUvsVirus/MINERVA-API/element_jsons/HMOX1 pathway_annotations.json, Analysis/EUvsVirus/MINERVA-API/element_jsons/Interferon 2 pathway_annotations.json, Analysis/EUvsVirus/MINERVA-API/element_jsons/Nsp14 and metabolism_annotations.json, Analysis/EUvsVirus/MINERVA-API/element_jsons/Nsp4 and Nsp6 interactions_annotations.json, Analysis/EUvsVirus/MINERVA-API/element_jsons/Orf10 Cul2 pathway_annotations.json, Analysis/EUvsVirus/MINERVA-API/element_jsons/PAMP signaling_annotations.json, Analysis/EUvsVirus/MINERVA-API/element_jsons/RTC and transcription_annotations.json, Analysis/EUvsVirus/MINERVA-API/element_jsons/Type I Ifn signaling (WP4868)_annotations.json, Analysis/EUvsVirus/MINERVA-API/element_jsons/Virus replication cycle_annotations.json, Analysis/EUvsVirus/MINERVA-API/element_jsons/overview_annotations.json, Analysis/EUvsVirus/MINERVA-API/overlays/all_MINERVA_targets.txt, Analysis/EUvsVirus/MINERVA-API/overlays/eNIOS_downregulated_genes.txt, Analysis/EUvsVirus/MINERVA-API/overlays/eNIOS_drug_targets.txt, Analysis/EUvsVirus/MINERVA-API/overlays/eNIOS_upregulated_genes.txt, Analysis/EUvsVirus/MINERVA-API/overlays/textmining_drug_targets.txt, Analysis/EUvsVirus/MINERVA-API/ACE2-Spike-drugs.txt, Analysis/EUvsVirus/MINERVA-API/Apoptosis.txt, Analysis/EUvsVirus/MINERVA-API/ER stress.txt, Analysis/EUvsVirus/MINERVA-API/HCoVs ER stress (WP4869).txt, Analysis/EUvsVirus/MINERVA-API/HCoVs autophagy (WP4863).txt, Analysis/EUvsVirus/MINERVA-API/Ifn 2 pathway drug targets MINERVA.txt, Analysis/EUvsVirus/MINERVA-API/Influenza-Cytokine-storm_Textmining_2018.gpml, Analysis/EUvsVirus/MINERVA-API/Interferon 2 pathway.txt, Analysis/EUvsVirus/MINERVA-API/Nsp14 and metabolism.txt, Analysis/EUvsVirus/MINERVA-API/Nsp4 and Nsp6 interactions.txt, Analysis/EUvsVirus/MINERVA-API/Orf10 Cul2 pathway.txt, Analysis/EUvsVirus/MINERVA-API/PAMP signaling.txt, Analysis/EUvsVirus/MINERVA-API/Type I Ifn signaling (WP4868).txt, Analysis/EUvsVirus/MINERVA-API/Virus replication cycle.txt, Analysis/EUvsVirus/MINERVA-API/drug_targets.R, Analysis/EUvsVirus/MINERVA-API/generate_SBML.R, Analysis/EUvsVirus/MINERVA-API/hackathon_covid19_map_v3-elementExport.txt, Analysis/EUvsVirus/MINERVA-API/map_cytstorm.txt, Analysis/EUvsVirus/MergedModels/.gitkeep, Analysis/EUvsVirus/MergedModels/Apoptosis_VS_SSA_AN_drugs_mirna.xml, Analysis/EUvsVirus/MergedModels/COVID19_PAMP_signaling_drugs_mirna.xml, Analysis/EUvsVirus/MergedModels/ER_Stress_drugs_mirna.xml, Analysis/EUvsVirus/MergedModels/Interferon2_drugs_mirna.xml, Analysis/EUvsVirus/Overlays_Updated_Vid/.gitkeep, Analysis/EUvsVirus/Overlays_Updated_Vid/ER_stress_drugs_enios.txt, Analysis/EUvsVirus/Overlays_Updated_Vid/ER_stress_text_mining_drugs.txt, Analysis/EUvsVirus/Overlays_Updated_Vid/InterferonEniosListWithDrug.txt, Analysis/EUvsVirus/Overlays_Updated_Vid/InterferonTextMiningListWithDrug.txt, Analysis/EUvsVirus/Overlays_Updated_Vid/Overlay_ER_Stress_Downregulated.txt, Analysis/EUvsVirus/Overlays_Updated_Vid/Overlay_ER_Stress_Upregulated.txt, Analysis/EUvsVirus/Overlays_Updated_Vid/Overlay_IFN_downregulated.txt, Analysis/EUvsVirus/Overlays_Updated_Vid/Overlay_IFN_upregulated.txt, Analysis/EUvsVirus/Overlays_Updated_Vid/Overlay_PAMP_Downregulated.txt, Analysis/EUvsVirus/Overlays_Updated_Vid/Overlay_PAMP_Upregulated.txt, Analysis/EUvsVirus/Overlays_Updated_Vid/PAMP_enios_drugs.txt, Analysis/EUvsVirus/Overlays_Updated_Vid/PAMP_text_mining_drugs.txt, Analysis/EUvsVirus/Overlays_Updated_Vid/apoptosis_enios_drug_target.txt, Analysis/EUvsVirus/Overlays_Updated_Vid/apoptosis_text_mining_drug_target.txt, Analysis/EUvsVirus/Overlays_Updated_Vid/downregulated_apoptosis_enios.txt, Analysis/EUvsVirus/Overlays_Updated_Vid/upregulated_apoptosis_enios.txt, Analysis/EUvsVirus/Hackathon workflow.png, Analysis/EUvsVirus/Readme.md, Analysis/Readme.md files

Analysis/Readme.md

+# Contents of the 'Analysis' folder
+- **EUvsVirus** folder contains our code, data and models developed during the EUvsVirus hackathon

Readme.md

@@ -2,12 +2,13 @@
 
 This repository is to share models and code for the analysis of COVID-19/SARS-CoV-2 mechanisms.
 
+- **Analysis** folder is dedicated to analytical workflows for the content of the map
 - **Curation** folder contains models curated in CellDesigner, Newt and SBGN-ED
-- **Integration** folder contains the workflow for building a single map from multiple modules
-- **EUvsVirus** folder contains our code, data and models developed during the EUvsVirus hackathon
 - **Executable models** folder contains Boolean models of COVID-19 curated diagrams generated with CaSQ
+- **Integration** folder contains the workflow for building a single map from multiple modules
+- **Resources** folder contains scripts demonstrating integration of COVID-19 Disease Map diagrams with other bioinformatic resources  
 - **WikiPathways** folder contains a list of key COVID19 pathways on the [WikiPathways platform](https://wikipathways.org), 
 a dedicated collection [here](https://www.wikipathways.org/index.php/Portal:Disease/COVIDPathways).
 Also, the folder contains examples of conversion of WikiPathways GPML to CellDesigner
 
-See the [COVID-19 Disease Map project website](https://covid.pages.uni.lu/map_curation) for more information.
\ No newline at end of file
+See the [COVID-19 Disease Map project website](https://covid.pages.uni.lu/map_curation) for more information.