Revised dir structure

Merge branch 'master' into repo_update

Revised dir structure
Merge branch 'master' into repo_update
5d849b0e · Marek Ostaszewski · d63ba69c · b2fb54e6 · 5d849b0e · 5d849b0e
Commit 5d849b0e authored Feb 13, 2021 by Marek Ostaszewski
132 changed files
--- a/EUvsVirus/Covid19KG_Fraunhofer_Hipathia/.gitkeep
+++ b/EUvsVirus/Covid19KG_Fraunhofer_Hipathia/.gitkeep
--- a/EUvsVirus/GMLs_AF__four_maps/.gitkeep
+++ b/EUvsVirus/GMLs_AF__four_maps/.gitkeep
--- a/EUvsVirus/GMLs_AF__four_maps/Apoptosis.gml
+++ b/EUvsVirus/GMLs_AF__four_maps/Apoptosis.gml
--- a/EUvsVirus/GMLs_AF__four_maps/Apoptosis_AF.pdf
+++ b/EUvsVirus/GMLs_AF__four_maps/Apoptosis_AF.pdf
--- a/EUvsVirus/GMLs_AF__four_maps/ER-stress.gml
+++ b/EUvsVirus/GMLs_AF__four_maps/ER-stress.gml
--- a/EUvsVirus/GMLs_AF__four_maps/ER-stress_AF.pdf
+++ b/EUvsVirus/GMLs_AF__four_maps/ER-stress_AF.pdf
--- a/EUvsVirus/GMLs_AF__four_maps/Interferon.gml
+++ b/EUvsVirus/GMLs_AF__four_maps/Interferon.gml
--- a/EUvsVirus/GMLs_AF__four_maps/Interferon_AF.pdf
+++ b/EUvsVirus/GMLs_AF__four_maps/Interferon_AF.pdf
--- a/EUvsVirus/GMLs_AF__four_maps/PAMP.graphml
+++ b/EUvsVirus/GMLs_AF__four_maps/PAMP.graphml
--- a/EUvsVirus/GMLs_AF__four_maps/PAMP_AF.pdf
+++ b/EUvsVirus/GMLs_AF__four_maps/PAMP_AF.pdf
--- a/EUvsVirus/Hackathon workflow.png
+++ b/EUvsVirus/Hackathon workflow.png
--- a/EUvsVirus/Hipathia_maps/.gitkeep
+++ b/EUvsVirus/Hipathia_maps/.gitkeep
--- a/EUvsVirus/Hipathia_operableMaps/.gitkeep
+++ b/EUvsVirus/Hipathia_operableMaps/.gitkeep
--- a/EUvsVirus/Hipathia_operableMaps/hsaCovid19KG.att
+++ b/EUvsVirus/Hipathia_operableMaps/hsaCovid19KG.att
--- a/EUvsVirus/Hipathia_operableMaps/hsaCovid19KG.sif
+++ b/EUvsVirus/Hipathia_operableMaps/hsaCovid19KG.sif
--- a/EUvsVirus/MINERVA-API/ACE2-Spike-drugs.txt
+++ b/EUvsVirus/MINERVA-API/ACE2-Spike-drugs.txt
--- a/EUvsVirus/MINERVA-API/Apoptosis.txt
+++ b/EUvsVirus/MINERVA-API/Apoptosis.txt
--- a/EUvsVirus/MINERVA-API/ER stress.txt
+++ b/EUvsVirus/MINERVA-API/ER stress.txt
--- a/EUvsVirus/MINERVA-API/HCoVs ER stress (WP4869).txt
+++ b/EUvsVirus/MINERVA-API/HCoVs ER stress (WP4869).txt
--- a/EUvsVirus/MINERVA-API/HCoVs autophagy (WP4863).txt
+++ b/EUvsVirus/MINERVA-API/HCoVs autophagy (WP4863).txt
--- a/EUvsVirus/MINERVA-API/Ifn 2 pathway drug targets MINERVA.txt
+++ b/EUvsVirus/MINERVA-API/Ifn 2 pathway drug targets MINERVA.txt
--- a/EUvsVirus/MINERVA-API/Influenza-Cytokine-storm_Textmining_2018.gpml
+++ b/EUvsVirus/MINERVA-API/Influenza-Cytokine-storm_Textmining_2018.gpml
--- a/EUvsVirus/MINERVA-API/Interferon 2 pathway.txt
+++ b/EUvsVirus/MINERVA-API/Interferon 2 pathway.txt
--- a/EUvsVirus/MINERVA-API/Nsp14 and metabolism.txt
+++ b/EUvsVirus/MINERVA-API/Nsp14 and metabolism.txt
--- a/EUvsVirus/MINERVA-API/Nsp4 and Nsp6 interactions.txt
+++ b/EUvsVirus/MINERVA-API/Nsp4 and Nsp6 interactions.txt
--- a/EUvsVirus/MINERVA-API/Orf10 Cul2 pathway.txt
+++ b/EUvsVirus/MINERVA-API/Orf10 Cul2 pathway.txt
--- a/EUvsVirus/MINERVA-API/PAMP signaling.txt
+++ b/EUvsVirus/MINERVA-API/PAMP signaling.txt
--- a/EUvsVirus/MINERVA-API/Type I Ifn signaling (WP4868).txt
+++ b/EUvsVirus/MINERVA-API/Type I Ifn signaling (WP4868).txt
--- a/EUvsVirus/MINERVA-API/Virus replication cycle.txt
+++ b/EUvsVirus/MINERVA-API/Virus replication cycle.txt
--- a/EUvsVirus/MINERVA-API/drug_targets.R
+++ b/EUvsVirus/MINERVA-API/drug_targets.R
--- a/EUvsVirus/MINERVA-API/drug_targets/ACE2-Spike-drugs.txt
+++ b/EUvsVirus/MINERVA-API/drug_targets/ACE2-Spike-drugs.txt
--- a/EUvsVirus/MINERVA-API/drug_targets/Apoptosis.txt
+++ b/EUvsVirus/MINERVA-API/drug_targets/Apoptosis.txt
--- a/EUvsVirus/MINERVA-API/drug_targets/ER stress.txt
+++ b/EUvsVirus/MINERVA-API/drug_targets/ER stress.txt
--- a/EUvsVirus/MINERVA-API/drug_targets/HCoVs ER stress (WP4869).txt
+++ b/EUvsVirus/MINERVA-API/drug_targets/HCoVs ER stress (WP4869).txt
--- a/EUvsVirus/MINERVA-API/drug_targets/HCoVs autophagy (WP4863).txt
+++ b/EUvsVirus/MINERVA-API/drug_targets/HCoVs autophagy (WP4863).txt
--- a/EUvsVirus/MINERVA-API/drug_targets/Interferon 2 pathway.txt
+++ b/EUvsVirus/MINERVA-API/drug_targets/Interferon 2 pathway.txt
--- a/EUvsVirus/MINERVA-API/drug_targets/Nsp14 and metabolism.txt
+++ b/EUvsVirus/MINERVA-API/drug_targets/Nsp14 and metabolism.txt
--- a/EUvsVirus/MINERVA-API/drug_targets/Nsp4 and Nsp6 interactions.txt
+++ b/EUvsVirus/MINERVA-API/drug_targets/Nsp4 and Nsp6 interactions.txt
--- a/EUvsVirus/MINERVA-API/drug_targets/Orf10 Cul2 pathway.txt
+++ b/EUvsVirus/MINERVA-API/drug_targets/Orf10 Cul2 pathway.txt
--- a/EUvsVirus/MINERVA-API/drug_targets/PAMP signaling.txt
+++ b/EUvsVirus/MINERVA-API/drug_targets/PAMP signaling.txt
--- a/EUvsVirus/MINERVA-API/drug_targets/Type I Ifn signaling (WP4868).txt
+++ b/EUvsVirus/MINERVA-API/drug_targets/Type I Ifn signaling (WP4868).txt
--- a/EUvsVirus/MINERVA-API/drug_targets/Virus replication cycle.txt
+++ b/EUvsVirus/MINERVA-API/drug_targets/Virus replication cycle.txt
--- a/EUvsVirus/MINERVA-API/element_jsons/ACE2-Spike-drugs_annotations.json
+++ b/EUvsVirus/MINERVA-API/element_jsons/ACE2-Spike-drugs_annotations.json
--- a/EUvsVirus/MINERVA-API/element_jsons/Apoptosis_annotations.json
+++ b/EUvsVirus/MINERVA-API/element_jsons/Apoptosis_annotations.json
--- a/EUvsVirus/MINERVA-API/element_jsons/ER stress_annotations.json
+++ b/EUvsVirus/MINERVA-API/element_jsons/ER stress_annotations.json
--- a/EUvsVirus/MINERVA-API/element_jsons/HCoVs ER stress (WP4869)_annotations.json
+++ b/EUvsVirus/MINERVA-API/element_jsons/HCoVs ER stress (WP4869)_annotations.json
--- a/EUvsVirus/MINERVA-API/element_jsons/HCoVs autophagy (WP4863)_annotations.json
+++ b/EUvsVirus/MINERVA-API/element_jsons/HCoVs autophagy (WP4863)_annotations.json
--- a/EUvsVirus/MINERVA-API/element_jsons/HMOX1 pathway_annotations.json
+++ b/EUvsVirus/MINERVA-API/element_jsons/HMOX1 pathway_annotations.json
--- a/EUvsVirus/MINERVA-API/element_jsons/Interferon 2 pathway_annotations.json
+++ b/EUvsVirus/MINERVA-API/element_jsons/Interferon 2 pathway_annotations.json
--- a/EUvsVirus/MINERVA-API/element_jsons/Nsp14 and metabolism_annotations.json
+++ b/EUvsVirus/MINERVA-API/element_jsons/Nsp14 and metabolism_annotations.json
--- a/EUvsVirus/MINERVA-API/element_jsons/Nsp4 and Nsp6 interactions_annotations.json
+++ b/EUvsVirus/MINERVA-API/element_jsons/Nsp4 and Nsp6 interactions_annotations.json
--- a/EUvsVirus/MINERVA-API/element_jsons/Orf10 Cul2 pathway_annotations.json
+++ b/EUvsVirus/MINERVA-API/element_jsons/Orf10 Cul2 pathway_annotations.json
--- a/EUvsVirus/MINERVA-API/element_jsons/PAMP signaling_annotations.json
+++ b/EUvsVirus/MINERVA-API/element_jsons/PAMP signaling_annotations.json
--- a/EUvsVirus/MINERVA-API/element_jsons/RTC and transcription_annotations.json
+++ b/EUvsVirus/MINERVA-API/element_jsons/RTC and transcription_annotations.json
--- a/EUvsVirus/MINERVA-API/element_jsons/Type I Ifn signaling (WP4868)_annotations.json
+++ b/EUvsVirus/MINERVA-API/element_jsons/Type I Ifn signaling (WP4868)_annotations.json
--- a/EUvsVirus/MINERVA-API/element_jsons/Virus replication cycle_annotations.json
+++ b/EUvsVirus/MINERVA-API/element_jsons/Virus replication cycle_annotations.json
--- a/EUvsVirus/MINERVA-API/element_jsons/overview_annotations.json
+++ b/EUvsVirus/MINERVA-API/element_jsons/overview_annotations.json
--- a/EUvsVirus/MINERVA-API/generate_SBML.R
+++ b/EUvsVirus/MINERVA-API/generate_SBML.R
--- a/EUvsVirus/MINERVA-API/hackathon_covid19_map_v3-elementExport.txt
+++ b/EUvsVirus/MINERVA-API/hackathon_covid19_map_v3-elementExport.txt
--- a/EUvsVirus/MINERVA-API/map_cytstorm.txt
+++ b/EUvsVirus/MINERVA-API/map_cytstorm.txt
--- a/EUvsVirus/MINERVA-API/overlays/all_MINERVA_targets.txt
+++ b/EUvsVirus/MINERVA-API/overlays/all_MINERVA_targets.txt
--- a/EUvsVirus/MINERVA-API/overlays/eNIOS_downregulated_genes.txt
+++ b/EUvsVirus/MINERVA-API/overlays/eNIOS_downregulated_genes.txt
--- a/EUvsVirus/MINERVA-API/overlays/eNIOS_drug_targets.txt
+++ b/EUvsVirus/MINERVA-API/overlays/eNIOS_drug_targets.txt
--- a/EUvsVirus/MINERVA-API/overlays/eNIOS_upregulated_genes.txt
+++ b/EUvsVirus/MINERVA-API/overlays/eNIOS_upregulated_genes.txt
--- a/EUvsVirus/MINERVA-API/overlays/textmining_drug_targets.txt
+++ b/EUvsVirus/MINERVA-API/overlays/textmining_drug_targets.txt
--- a/EUvsVirus/MergedModels/.gitkeep
+++ b/EUvsVirus/MergedModels/.gitkeep
--- a/EUvsVirus/MergedModels/Apoptosis_VS_SSA_AN_drugs_mirna.xml
+++ b/EUvsVirus/MergedModels/Apoptosis_VS_SSA_AN_drugs_mirna.xml
--- a/EUvsVirus/MergedModels/COVID19_PAMP_signaling_drugs_mirna.xml
+++ b/EUvsVirus/MergedModels/COVID19_PAMP_signaling_drugs_mirna.xml
--- a/EUvsVirus/MergedModels/ER_Stress_drugs_mirna.xml
+++ b/EUvsVirus/MergedModels/ER_Stress_drugs_mirna.xml
--- a/EUvsVirus/MergedModels/Interferon2_drugs_mirna.xml
+++ b/EUvsVirus/MergedModels/Interferon2_drugs_mirna.xml
--- a/EUvsVirus/Overlays_Updated_Vid/.gitkeep
+++ b/EUvsVirus/Overlays_Updated_Vid/.gitkeep
--- a/EUvsVirus/Overlays_Updated_Vid/ER_stress_drugs_enios.txt
+++ b/EUvsVirus/Overlays_Updated_Vid/ER_stress_drugs_enios.txt
--- a/EUvsVirus/Overlays_Updated_Vid/ER_stress_text_mining_drugs.txt
+++ b/EUvsVirus/Overlays_Updated_Vid/ER_stress_text_mining_drugs.txt
--- a/EUvsVirus/Overlays_Updated_Vid/InterferonEniosListWithDrug.txt
+++ b/EUvsVirus/Overlays_Updated_Vid/InterferonEniosListWithDrug.txt
--- a/EUvsVirus/Overlays_Updated_Vid/InterferonTextMiningListWithDrug.txt
+++ b/EUvsVirus/Overlays_Updated_Vid/InterferonTextMiningListWithDrug.txt
--- a/EUvsVirus/Overlays_Updated_Vid/Overlay_ER_Stress_Downregulated.txt
+++ b/EUvsVirus/Overlays_Updated_Vid/Overlay_ER_Stress_Downregulated.txt
--- a/EUvsVirus/Overlays_Updated_Vid/Overlay_ER_Stress_Upregulated.txt
+++ b/EUvsVirus/Overlays_Updated_Vid/Overlay_ER_Stress_Upregulated.txt
--- a/EUvsVirus/Overlays_Updated_Vid/Overlay_IFN_downregulated.txt
+++ b/EUvsVirus/Overlays_Updated_Vid/Overlay_IFN_downregulated.txt
--- a/EUvsVirus/Overlays_Updated_Vid/Overlay_IFN_upregulated.txt
+++ b/EUvsVirus/Overlays_Updated_Vid/Overlay_IFN_upregulated.txt
--- a/EUvsVirus/Overlays_Updated_Vid/Overlay_PAMP_Downregulated.txt
+++ b/EUvsVirus/Overlays_Updated_Vid/Overlay_PAMP_Downregulated.txt
--- a/EUvsVirus/Overlays_Updated_Vid/Overlay_PAMP_Upregulated.txt
+++ b/EUvsVirus/Overlays_Updated_Vid/Overlay_PAMP_Upregulated.txt
--- a/EUvsVirus/Overlays_Updated_Vid/PAMP_enios_drugs.txt
+++ b/EUvsVirus/Overlays_Updated_Vid/PAMP_enios_drugs.txt
--- a/EUvsVirus/Overlays_Updated_Vid/PAMP_text_mining_drugs.txt
+++ b/EUvsVirus/Overlays_Updated_Vid/PAMP_text_mining_drugs.txt
--- a/EUvsVirus/Overlays_Updated_Vid/apoptosis_enios_drug_target.txt
+++ b/EUvsVirus/Overlays_Updated_Vid/apoptosis_enios_drug_target.txt
--- a/EUvsVirus/Overlays_Updated_Vid/apoptosis_text_mining_drug_target.txt
+++ b/EUvsVirus/Overlays_Updated_Vid/apoptosis_text_mining_drug_target.txt
--- a/EUvsVirus/Overlays_Updated_Vid/downregulated_apoptosis_enios.txt
+++ b/EUvsVirus/Overlays_Updated_Vid/downregulated_apoptosis_enios.txt
--- a/EUvsVirus/Overlays_Updated_Vid/upregulated_apoptosis_enios.txt
+++ b/EUvsVirus/Overlays_Updated_Vid/upregulated_apoptosis_enios.txt
--- a/EUvsVirus/Readme.md
+++ b/EUvsVirus/Readme.md
--- a/Analysis/Readme.md
+++ b/Analysis/Readme.md
+# Contents of the 'Analysis' folder
+- **EUvsVirus** folder contains our code, data and models developed during the EUvsVirus hackathon
--- a/Executable Modules/SBML_qual_build/sif/Apoptosis_stable.sif
+++ b/Executable Modules/SBML_qual_build/sif/Apoptosis_stable.sif
-# Generated by CaSQ v0.9.6
+# Generated by CaSQ v0.9.7
 FAS/FASL_complex POSITIVE FADD
 BAD/BBC3/BCL2L11_complex POSITIVE BAX
 BCL2/MCL1/BCL2L1_complex POSITIVE BAD/BBC3/BCL2L11_complex

--- a/Executable Modules/SBML_qual_build/sif/Apoptosis_stable_raw.sif
+++ b/Executable Modules/SBML_qual_build/sif/Apoptosis_stable_raw.sif
-# Generated by CaSQ v0.9.6
+# Generated by CaSQ v0.9.7
 csa2 POSITIVE sa9
 csa3 POSITIVE sa30
 csa11 POSITIVE csa3

--- a/Executable Modules/SBML_qual_build/sif/Coagulation-pathway_stable.sif
+++ b/Executable Modules/SBML_qual_build/sif/Coagulation-pathway_stable.sif
-# Generated by CaSQ v0.9.6
+# Generated by CaSQ v0.9.7
 KNG1:KLKB1_complex POSITIVE Kininogen
 KNG1:KLKB1_complex POSITIVE Kallikrein
 KNG1:KLKB1_complex POSITIVE Bradykinin

--- a/Executable Modules/SBML_qual_build/sif/Coagulation-pathway_stable_raw.sif
+++ b/Executable Modules/SBML_qual_build/sif/Coagulation-pathway_stable_raw.sif
-# Generated by CaSQ v0.9.6
+# Generated by CaSQ v0.9.7
 csa11 POSITIVE sa250
 csa11 POSITIVE sa251
 csa11 POSITIVE sa402

--- a/Executable Modules/SBML_qual_build/sif/ER_Stress_stable.sif
+++ b/Executable Modules/SBML_qual_build/sif/ER_Stress_stable.sif
-# Generated by CaSQ v0.9.6
+# Generated by CaSQ v0.9.7
 EIF2-P:GDP_complex POSITIVE ATF4_rna
 EIF2S1_phosphorylated POSITIVE EIF2-P:GDP_complex
 EIF2S1_phosphorylated POSITIVE EIF2S1

--- a/Executable Modules/SBML_qual_build/sif/ER_Stress_stable_raw.sif
+++ b/Executable Modules/SBML_qual_build/sif/ER_Stress_stable_raw.sif
-# Generated by CaSQ v0.9.6
+# Generated by CaSQ v0.9.7
 path_0_csa33 POSITIVE path_0_sa106
 path_0_sa87 POSITIVE path_0_csa33
 path_0_sa87 POSITIVE path_0_sa90

--- a/Executable Modules/SBML_qual_build/sif/ETC_stable.sif
+++ b/Executable Modules/SBML_qual_build/sif/ETC_stable.sif
-# Generated by CaSQ v0.9.6
+# Generated by CaSQ v0.9.7
 Complex_1_complex POSITIVE Complex_1_complex
 Complex_1_complex POSITIVE complex_2_complex_mitochondrial_matrix
 Complex_1_complex POSITIVE complex_3_complex

--- a/Executable Modules/SBML_qual_build/sif/ETC_stable_raw.sif
+++ b/Executable Modules/SBML_qual_build/sif/ETC_stable_raw.sif
-# Generated by CaSQ v0.9.6
+# Generated by CaSQ v0.9.7
 csa20 POSITIVE csa20
 csa20 POSITIVE csa24
 csa20 POSITIVE csa34

--- a/Executable Modules/SBML_qual_build/sif/E_protein_stable.sif
+++ b/Executable Modules/SBML_qual_build/sif/E_protein_stable.sif
-# Generated by CaSQ v0.9.6
+# Generated by CaSQ v0.9.7
 histone_complex_Nucleus POSITIVE Chromatin_organization_phenotype
 histone_complex_Nucleus POSITIVE histone_complex_Nucleus
 BRD4 POSITIVE histone_complex_Nucleus

--- a/Executable Modules/SBML_qual_build/sif/E_protein_stable_raw.sif
+++ b/Executable Modules/SBML_qual_build/sif/E_protein_stable_raw.sif
-# Generated by CaSQ v0.9.6
+# Generated by CaSQ v0.9.7
 csa1 POSITIVE sa78
 csa2 POSITIVE csa1
 sa12 POSITIVE csa1

--- a/Executable Modules/SBML_qual_build/sif/HMOX1_Pathway_stable.sif
+++ b/Executable Modules/SBML_qual_build/sif/HMOX1_Pathway_stable.sif
-# Generated by CaSQ v0.9.6
+# Generated by CaSQ v0.9.7
 Nrf2/Maf_complex POSITIVE HMOX1_rna
 NRF2_phosphorylated_Nucleus POSITIVE Nrf2/Maf_complex
 NRF2_phosphorylated_Nucleus POSITIVE SLC40A1_rna

--- a/Executable Modules/SBML_qual_build/sif/HMOX1_Pathway_stable_raw.sif
+++ b/Executable Modules/SBML_qual_build/sif/HMOX1_Pathway_stable_raw.sif
--- a/Executable Modules/SBML_qual_build/sif/IFN-lambda_stable.sif
+++ b/Executable Modules/SBML_qual_build/sif/IFN-lambda_stable.sif
--- a/Executable Modules/SBML_qual_build/sif/IFN-lambda_stable_raw.sif
+++ b/Executable Modules/SBML_qual_build/sif/IFN-lambda_stable_raw.sif
--- a/Executable Modules/SBML_qual_build/sif/Interferon1_stable.sif
+++ b/Executable Modules/SBML_qual_build/sif/Interferon1_stable.sif
--- a/Executable Modules/SBML_qual_build/sif/Interferon1_stable_raw.sif
+++ b/Executable Modules/SBML_qual_build/sif/Interferon1_stable_raw.sif
--- a/Executable Modules/SBML_qual_build/sif/JNK_pathway_stable.sif
+++ b/Executable Modules/SBML_qual_build/sif/JNK_pathway_stable.sif
--- a/Executable Modules/SBML_qual_build/sif/JNK_pathway_stable_raw.sif
+++ b/Executable Modules/SBML_qual_build/sif/JNK_pathway_stable_raw.sif
--- a/Executable Modules/SBML_qual_build/sif/Kynurenine_pathway_stable.sif
+++ b/Executable Modules/SBML_qual_build/sif/Kynurenine_pathway_stable.sif
--- a/Executable Modules/SBML_qual_build/sif/Kynurenine_pathway_stable_raw.sif
+++ b/Executable Modules/SBML_qual_build/sif/Kynurenine_pathway_stable_raw.sif
--- a/Executable Modules/SBML_qual_build/sif/NLRP3_Activation_stable.sif
+++ b/Executable Modules/SBML_qual_build/sif/NLRP3_Activation_stable.sif
--- a/Executable Modules/SBML_qual_build/sif/NLRP3_Activation_stable_raw.sif
+++ b/Executable Modules/SBML_qual_build/sif/NLRP3_Activation_stable_raw.sif
--- a/Executable Modules/SBML_qual_build/sif/Nsp4_Nsp6_stable.sif
+++ b/Executable Modules/SBML_qual_build/sif/Nsp4_Nsp6_stable.sif
--- a/Executable Modules/SBML_qual_build/sif/Nsp4_Nsp6_stable_raw.sif
+++ b/Executable Modules/SBML_qual_build/sif/Nsp4_Nsp6_stable_raw.sif
--- a/Executable Modules/SBML_qual_build/sif/Nsp9_protein_stable.sif
+++ b/Executable Modules/SBML_qual_build/sif/Nsp9_protein_stable.sif
--- a/Executable Modules/SBML_qual_build/sif/Nsp9_protein_stable_raw.sif
+++ b/Executable Modules/SBML_qual_build/sif/Nsp9_protein_stable_raw.sif
--- a/Executable Modules/SBML_qual_build/sif/Orf10_Cul2_pathway_stable.sif
+++ b/Executable Modules/SBML_qual_build/sif/Orf10_Cul2_pathway_stable.sif
--- a/Executable Modules/SBML_qual_build/sif/Orf10_Cul2_pathway_stable_raw.sif
+++ b/Executable Modules/SBML_qual_build/sif/Orf10_Cul2_pathway_stable_raw.sif
--- a/Executable Modules/SBML_qual_build/sif/Orf3a_stable.sif
+++ b/Executable Modules/SBML_qual_build/sif/Orf3a_stable.sif
--- a/Executable Modules/SBML_qual_build/sif/Orf3a_stable_raw.sif
+++ b/Executable Modules/SBML_qual_build/sif/Orf3a_stable_raw.sif
--- a/Executable Modules/SBML_qual_build/sif/PAMP_signaling_stable.sif
+++ b/Executable Modules/SBML_qual_build/sif/PAMP_signaling_stable.sif
--- a/Executable Modules/SBML_qual_build/sif/PAMP_signaling_stable_raw.sif
+++ b/Executable Modules/SBML_qual_build/sif/PAMP_signaling_stable_raw.sif
--- a/Executable Modules/SBML_qual_build/sif/Pyrimidine_deprivation_stable.sif
+++ b/Executable Modules/SBML_qual_build/sif/Pyrimidine_deprivation_stable.sif
--- a/Executable Modules/SBML_qual_build/sif/Pyrimidine_deprivation_stable_raw.sif
+++ b/Executable Modules/SBML_qual_build/sif/Pyrimidine_deprivation_stable_raw.sif
--- a/Executable Modules/SBML_qual_build/sif/RTC-and-transcription_stable.sif
+++ b/Executable Modules/SBML_qual_build/sif/RTC-and-transcription_stable.sif
--- a/Executable Modules/SBML_qual_build/sif/RTC-and-transcription_stable_raw.sif
+++ b/Executable Modules/SBML_qual_build/sif/RTC-and-transcription_stable_raw.sif
--- a/Executable Modules/SBML_qual_build/sif/Renin_angiotensin_stable.sif
+++ b/Executable Modules/SBML_qual_build/sif/Renin_angiotensin_stable.sif
--- a/Executable Modules/SBML_qual_build/sif/Renin_angiotensin_stable_raw.sif
+++ b/Executable Modules/SBML_qual_build/sif/Renin_angiotensin_stable_raw.sif
--- a/Executable Modules/SBML_qual_build/sif/TGFB_pathway_stable.sif
+++ b/Executable Modules/SBML_qual_build/sif/TGFB_pathway_stable.sif
--- a/Executable Modules/SBML_qual_build/sif/TGFB_pathway_stable_raw.sif
+++ b/Executable Modules/SBML_qual_build/sif/TGFB_pathway_stable_raw.sif
--- a/Executable Modules/SBML_qual_build/sif/Virus_replication_cycle_stable.sif
+++ b/Executable Modules/SBML_qual_build/sif/Virus_replication_cycle_stable.sif
--- a/Executable Modules/SBML_qual_build/sif/Virus_replication_cycle_stable_raw.sif
+++ b/Executable Modules/SBML_qual_build/sif/Virus_replication_cycle_stable_raw.sif
--- a/Readme.md
+++ b/Readme.md