Merge branch 'repo_update' into 'master'

smaller crosstalks

See merge request !264

Executable Modules/SBML_qual_build/sif/Apoptosis_stable.sif

-# Generated by CaSQ v0.9.2
+# Generated by CaSQ v0.9.3
 FAS/FASL_complex POSITIVE FADD
 BAD/BBC3/BCL2L11_complex POSITIVE BAX
 BCL2/MCL1/BCL2L1_complex POSITIVE BAD/BBC3/BCL2L11_complex

Executable Modules/SBML_qual_build/sif/Apoptosis_stable_raw.sif

-# Generated by CaSQ v0.9.2
+# Generated by CaSQ v0.9.3
 csa2 POSITIVE sa9
 csa3 POSITIVE sa30
 csa11 POSITIVE csa3

Executable Modules/SBML_qual_build/sif/Coagulation-pathway_stable.sif

-# Generated by CaSQ v0.9.2
+# Generated by CaSQ v0.9.3
 KNG1:KLKB1_complex POSITIVE Kininogen
 KNG1:KLKB1_complex POSITIVE Kallikrein
 KNG1:KLKB1_complex POSITIVE Bradykinin

Executable Modules/SBML_qual_build/sif/Coagulation-pathway_stable_raw.sif

-# Generated by CaSQ v0.9.2
+# Generated by CaSQ v0.9.3
 csa11 POSITIVE sa250
 csa11 POSITIVE sa251
 csa11 POSITIVE sa402

Executable Modules/SBML_qual_build/sif/ER_Stress_stable.sif

-# Generated by CaSQ v0.9.2
+# Generated by CaSQ v0.9.3
 EIF2-P:GDP_complex POSITIVE ATF4_rna
 EIF2S1_phosphorylated POSITIVE EIF2-P:GDP_complex
 EIF2S1_phosphorylated POSITIVE EIF2S1

Executable Modules/SBML_qual_build/sif/ER_Stress_stable_raw.sif

-# Generated by CaSQ v0.9.2
+# Generated by CaSQ v0.9.3
 path_0_csa33 POSITIVE path_0_sa106
 path_0_sa87 POSITIVE path_0_csa33
 path_0_sa87 POSITIVE path_0_sa90

Executable Modules/SBML_qual_build/sif/ETC_stable.sif

-# Generated by CaSQ v0.9.2
+# Generated by CaSQ v0.9.3
 Complex_1_complex POSITIVE Complex_1_complex
 Complex_1_complex POSITIVE complex_2_complex_mitochondrial_matrix
 Complex_1_complex POSITIVE complex_3_complex

Executable Modules/SBML_qual_build/sif/ETC_stable_raw.sif

-# Generated by CaSQ v0.9.2
+# Generated by CaSQ v0.9.3
 csa20 POSITIVE csa20
 csa20 POSITIVE csa24
 csa20 POSITIVE csa34

Executable Modules/SBML_qual_build/sif/E_protein_stable.sif

-# Generated by CaSQ v0.9.2
+# Generated by CaSQ v0.9.3
 histone_complex_Nucleus POSITIVE Chromatin_organization_phenotype
 histone_complex_Nucleus POSITIVE histone_complex_Nucleus
 BRD4 POSITIVE histone_complex_Nucleus

Executable Modules/SBML_qual_build/sif/E_protein_stable_raw.sif

-# Generated by CaSQ v0.9.2
+# Generated by CaSQ v0.9.3
 csa1 POSITIVE sa78
 csa2 POSITIVE csa1
 sa12 POSITIVE csa1

Executable Modules/SBML_qual_build/sif/HMOX1_Pathway_stable.sif

-# Generated by CaSQ v0.9.2
+# Generated by CaSQ v0.9.3
 Nrf2/Maf_complex POSITIVE HMOX1_rna
 NRF2_phosphorylated_Nucleus POSITIVE Nrf2/Maf_complex
 NRF2_phosphorylated_Nucleus POSITIVE SLC40A1_rna

Executable Modules/SBML_qual_build/sif/HMOX1_Pathway_stable_raw.sif

-# Generated by CaSQ v0.9.2
+# Generated by CaSQ v0.9.3
 csa2 POSITIVE sa50
 sa43 POSITIVE csa2
 sa43 POSITIVE sa140

Executable Modules/SBML_qual_build/sif/IFN-lambda_stable.sif

-# Generated by CaSQ v0.9.2
+# Generated by CaSQ v0.9.3
 receptor_complex_complex_cell POSITIVE receptor_complex_complex_cell
 receptor_complex_complex_cell POSITIVE receptor_complex_complex_cell
 receptor_complex_complex_cell POSITIVE ISGF3_precursor_complex

Executable Modules/SBML_qual_build/sif/IFN-lambda_stable_raw.sif

-# Generated by CaSQ v0.9.2
+# Generated by CaSQ v0.9.3
 csa10 POSITIVE csa9
 csa10 POSITIVE csa11
 csa10 POSITIVE csa12

Executable Modules/SBML_qual_build/sif/Interferon1_stable.sif

-# Generated by CaSQ v0.9.2
+# Generated by CaSQ v0.9.3
 IFNA1_IFNAR_complex POSITIVE JAK1_TYK2_complex
 IFNAR_complex POSITIVE IFNA1_IFNAR_complex
 IFNAR_complex POSITIVE IFNB1_IFNAR_complex

Executable Modules/SBML_qual_build/sif/Interferon1_stable_raw.sif

-# Generated by CaSQ v0.9.2
+# Generated by CaSQ v0.9.3
 csa2 POSITIVE csa9
 csa1 POSITIVE csa2
 csa1 POSITIVE csa3

Executable Modules/SBML_qual_build/sif/JNK_pathway_stable.sif

-# Generated by CaSQ v0.9.2
+# Generated by CaSQ v0.9.3
 JNK_complex_Cytoplasm POSITIVE AP-1_complex
 JNK_complex_Cytoplasm POSITIVE BCL2_phosphorylated
 JNK_complex_Cytoplasm POSITIVE ATF2_phosphorylated

Executable Modules/SBML_qual_build/sif/JNK_pathway_stable_raw.sif

-# Generated by CaSQ v0.9.2
+# Generated by CaSQ v0.9.3
 csa1 POSITIVE csa4
 csa1 POSITIVE sa12
 csa1 POSITIVE sa33

Executable Modules/SBML_qual_build/sif/Kynurenine_pathway_stable.sif

-# Generated by CaSQ v0.9.2
+# Generated by CaSQ v0.9.3
 AHR/L-KYN_complex POSITIVE Regulatory_T-cell_generation_phenotype
 L-Kynurenine_simple_molecule POSITIVE AHR/L-KYN_complex
 L-Kynurenine_simple_molecule POSITIVE H2O_simple_molecule_Cytosol

Executable Modules/SBML_qual_build/sif/Kynurenine_pathway_stable_raw.sif

-# Generated by CaSQ v0.9.2
+# Generated by CaSQ v0.9.3
 csa2 POSITIVE sa35
 sa17 POSITIVE csa2
 sa17 POSITIVE sa10

Executable Modules/SBML_qual_build/sif/Nsp4_Nsp6_stable.sif

-# Generated by CaSQ v0.9.2
+# Generated by CaSQ v0.9.3
 Nsp3:Nsp4:Nsp6_complex POSITIVE Plasma_membrane_organization_phenotype
 Nsp3 POSITIVE Nsp3:Nsp4:Nsp6_complex
 Nsp6 POSITIVE Nsp3:Nsp4:Nsp6_complex

Executable Modules/SBML_qual_build/sif/Nsp4_Nsp6_stable_raw.sif

-# Generated by CaSQ v0.9.2
+# Generated by CaSQ v0.9.3
 csa39 POSITIVE sa164
 sa162 POSITIVE csa39
 sa48 POSITIVE csa39

Executable Modules/SBML_qual_build/sif/Nsp9_protein_stable.sif

-# Generated by CaSQ v0.9.2
+# Generated by CaSQ v0.9.3
 Nsp9_cytoplasm POSITIVE Fibrillincomp_complex
 Nsp9_cytoplasm POSITIVE Nuclear_Pore_comp_complex
 Nsp9_cytoplasm POSITIVE mibcomp_complex

Executable Modules/SBML_qual_build/sif/Nsp9_protein_stable_raw.sif

-# Generated by CaSQ v0.9.2
+# Generated by CaSQ v0.9.3
 a7c94 POSITIVE csa17
 a7c94 POSITIVE csa21
 a7c94 POSITIVE csa28

Executable Modules/SBML_qual_build/sif/Orf10_Cul2_pathway_stable.sif

-# Generated by CaSQ v0.9.2
+# Generated by CaSQ v0.9.3
 Cul2_ubiquitin_ligase_complex POSITIVE Zyg11B:EloBC_complex
 Cul2_ubiquitin_ligase_complex POSITIVE Cul2_ubiquitin_ligase:Orf10_complex
 Cul2_ubiquitin_ligase_complex POSITIVE Cul2_ubiquitin_ligase:substrate_complex_cytosol

Executable Modules/SBML_qual_build/sif/Orf10_Cul2_pathway_stable_raw.sif

-# Generated by CaSQ v0.9.2
+# Generated by CaSQ v0.9.3
 csa5 POSITIVE csa2
 csa5 POSITIVE csa35
 csa5 POSITIVE csa4

Executable Modules/SBML_qual_build/sif/Orf3a_stable.sif

-# Generated by CaSQ v0.9.2
+# Generated by CaSQ v0.9.3
 Orf3a POSITIVE Hops_Complex_complex
 Orf3a POSITIVE P65/P015_complex
 Orf3a POSITIVE TRIM59

Executable Modules/SBML_qual_build/sif/Orf3a_stable_raw.sif

-# Generated by CaSQ v0.9.2
+# Generated by CaSQ v0.9.3
 sa1 POSITIVE csa2
 sa1 POSITIVE csa7
 sa1 POSITIVE sa3

Executable Modules/SBML_qual_build/sif/PAMP_signaling_stable.sif

-# Generated by CaSQ v0.9.2
+# Generated by CaSQ v0.9.3
 MYD88:IRAK:TRAF_complex POSITIVE IRF7_phosphorylated
 MYD88:IRAK:TRAF_complex POSITIVE TRAF6_ubiquitinated
 MYD88 POSITIVE MYD88:IRAK:TRAF_complex

Executable Modules/SBML_qual_build/sif/PAMP_signaling_stable_raw.sif

-# Generated by CaSQ v0.9.2
+# Generated by CaSQ v0.9.3
 csa56 POSITIVE sa255
 csa56 POSITIVE sa337
 sa77 POSITIVE csa56

Executable Modules/SBML_qual_build/sif/Pyrimidine_deprivation_stable.sif

-# Generated by CaSQ v0.9.2
+# Generated by CaSQ v0.9.3
 IFNB1_space_expression_space_complex_complex POSITIVE IFNA1_rna
 IFNB1_space_expression_space_complex_complex POSITIVE IFNB1_rna
 NF-kB_complex POSITIVE IFNB1_space_expression_space_complex_complex

Executable Modules/SBML_qual_build/sif/Pyrimidine_deprivation_stable_raw.sif

-# Generated by CaSQ v0.9.2
+# Generated by CaSQ v0.9.3
 csa8 POSITIVE sa88
 csa8 POSITIVE sa89
 csa19 POSITIVE csa8

Executable Modules/SBML_qual_build/sif/RTC-and-transcription_stable.sif

-# Generated by CaSQ v0.9.2
+# Generated by CaSQ v0.9.3
 Replication_space_transcription_space_complex_space__complex_double_space_membrane_space_vesicle_space_(DMV)_space_(builds_space_membrane_space_network_space_from_space_ER_space_membrane_space_and_space_accumulates_space_at_space_perinuclear_space_regions POSITIVE CoV_space_poly-br_merase_space_complex_complex_double_space_membrane_space_vesicle_space_(DMV)_space_(builds_space_membrane_space_network_space_from_space_ER_space_membrane_space_and_space_accumulates_space_at_space_perinuclear_space_regions
 Replication_space_transcription_space_complex_space__complex_double_space_membrane_space_vesicle_space_(DMV)_space_(builds_space_membrane_space_network_space_from_space_ER_space_membrane_space_and_space_accumulates_space_at_space_perinuclear_space_regions POSITIVE complex_complex_double_space_membrane_space_vesicle_space_(DMV)_space_(builds_space_membrane_space_network_space_from_space_ER_space_membrane_space_and_space_accumulates_space_at_space_perinuclear_space_regions
 Replication_space_transcription_space_complex_space__complex_double_space_membrane_space_vesicle_space_(DMV)_space_(builds_space_membrane_space_network_space_from_space_ER_space_membrane_space_and_space_accumulates_space_at_space_perinuclear_space_regions POSITIVE (+)gRNA_space_(including_space_ORF1a_space_ORF1b)_gene_double_space_membrane_space_vesicle_space_(DMV)_space_(builds_space_membrane_space_network_space_from_space_ER_space_membrane_space_and_space_accumulates_space_at_space_perinuclear_space_regions

Executable Modules/SBML_qual_build/sif/RTC-and-transcription_stable_raw.sif

-# Generated by CaSQ v0.9.2
+# Generated by CaSQ v0.9.3
 glyph2 POSITIVE glyph4
 glyph2 POSITIVE glyph6
 glyph2 POSITIVE glyph17

Executable Modules/SBML_qual_build/sif/Renin_angiotensin_stable.sif

-# Generated by CaSQ v0.9.2
+# Generated by CaSQ v0.9.3
 AGTR1_cytoplasm POSITIVE ACE2:AGTR1_complex
 AGTR1_cytoplasm POSITIVE AGTR1_cytoplasm_active
 ACE2_cytoplasm POSITIVE ACE2:AGTR1_complex

Executable Modules/SBML_qual_build/sif/Renin_angiotensin_stable_raw.sif

-# Generated by CaSQ v0.9.2
+# Generated by CaSQ v0.9.3
 sa26 POSITIVE csa4
 sa26 POSITIVE sa102
 sa30 POSITIVE csa4

Executable Modules/SBML_qual_build/sif/TGFB_pathway_stable.sif

-# Generated by CaSQ v0.9.2
+# Generated by CaSQ v0.9.3
 SMAD1/5/8_complex POSITIVE Modulation_Cell_Cycle_phenotype
 BAMBI NEGATIVE SMAD1/5/8_complex
 BAMBI NEGATIVE SMAD2/3_complex

Executable Modules/SBML_qual_build/sif/TGFB_pathway_stable_raw.sif

-# Generated by CaSQ v0.9.2
+# Generated by CaSQ v0.9.3
 csa3 POSITIVE sa55
 sa33 NEGATIVE csa3
 sa33 NEGATIVE csa5

Executable Modules/SBML_qual_build/sif/Virus_replication_cycle_stable.sif

-# Generated by CaSQ v0.9.2
+# Generated by CaSQ v0.9.3
 ACE2:SPIKE_complex_complex_EPITHELIAL_CELL POSITIVE Nucleocapsid_complex_SARS-CoV-2
 ACE2_EPITHELIAL_CELL POSITIVE ACE2:SPIKE_complex_complex_EPITHELIAL_CELL
 S_SARS-CoV-2 POSITIVE ACE2:SPIKE_complex_complex_EPITHELIAL_CELL

Executable Modules/SBML_qual_build/sif/Virus_replication_cycle_stable_raw.sif

-# Generated by CaSQ v0.9.2
+# Generated by CaSQ v0.9.3
 csa430 POSITIVE csa357
 sa1462 POSITIVE csa430
 sa1859 POSITIVE csa430