Merge branch 'clean_casq_build' into 'master'

Reset the auto-built files

See merge request !280

Executable Modules/SBML_qual_build/sif/Apoptosis_stable.sif

-# Generated by CaSQ v0.9.7
+# Generated by CaSQ v0.9.9
 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 v0.9.7
+# Generated by CaSQ v0.9.9
 csa2 POSITIVE sa9
 csa3 POSITIVE sa30
 csa11 POSITIVE csa3

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

-# Generated by CaSQ v0.9.7
+# Generated by CaSQ v0.9.9
 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 v0.9.7
+# Generated by CaSQ v0.9.9
 csa11 POSITIVE sa250
 csa11 POSITIVE sa251
 csa11 POSITIVE sa402

Executable Modules/SBML_qual_build/sif/ER_Stress_stable.sif

-# Generated by CaSQ v0.9.7
+# Generated by CaSQ v0.9.9
 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 v0.9.7
+# Generated by CaSQ v0.9.9
 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 v0.9.7
+# Generated by CaSQ v0.9.9
 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 v0.9.7
+# Generated by CaSQ v0.9.9
 csa20 POSITIVE csa20
 csa20 POSITIVE csa24
 csa20 POSITIVE csa34

Executable Modules/SBML_qual_build/sif/E_protein_stable.sif

-# Generated by CaSQ v0.9.7
+# Generated by CaSQ v0.9.9
 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 v0.9.7
+# Generated by CaSQ v0.9.9
 csa1 POSITIVE sa78
 csa2 POSITIVE csa1
 sa12 POSITIVE csa1

Executable Modules/SBML_qual_build/sif/HMOX1_Pathway_stable.sif

-# Generated by CaSQ v0.9.7
+# Generated by CaSQ v0.9.9
 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 v0.9.7
+# Generated by CaSQ v0.9.9
 csa2 POSITIVE sa50
 sa43 POSITIVE csa2
 sa43 POSITIVE sa140

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

-# Generated by CaSQ v0.9.7
+# Generated by CaSQ v0.9.9
 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 v0.9.7
+# Generated by CaSQ v0.9.9
 csa10 POSITIVE csa9
 csa10 POSITIVE csa11
 csa10 POSITIVE csa12

Executable Modules/SBML_qual_build/sif/Interferon1_stable.sif

-# Generated by CaSQ v0.9.7
+# Generated by CaSQ v0.9.9
 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 v0.9.7
+# Generated by CaSQ v0.9.9
 csa2 POSITIVE csa9
 csa1 POSITIVE csa2
 csa1 POSITIVE csa3

Executable Modules/SBML_qual_build/sif/JNK_pathway_stable.sif

-# Generated by CaSQ v0.9.7
+# Generated by CaSQ v0.9.9
 JNK_complex_cell POSITIVE AP-1_complex
 JNK_complex_cell POSITIVE BCL2_phosphorylated
 JNK_complex_cell POSITIVE ATF2_phosphorylated

Executable Modules/SBML_qual_build/sif/JNK_pathway_stable_raw.sif

-# Generated by CaSQ v0.9.7
+# Generated by CaSQ v0.9.9
 csa1 POSITIVE csa4
 csa1 POSITIVE sa12
 csa1 POSITIVE sa33

Executable Modules/SBML_qual_build/sif/Kynurenine_pathway_stable.sif

-# Generated by CaSQ v0.9.7
+# Generated by CaSQ v0.9.9
 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_cell

Executable Modules/SBML_qual_build/sif/Kynurenine_pathway_stable_raw.sif

-# Generated by CaSQ v0.9.7
+# Generated by CaSQ v0.9.9
 csa2 POSITIVE sa35
 sa17 POSITIVE csa2
 sa17 POSITIVE sa10

Executable Modules/SBML_qual_build/sif/NLRP3_Activation_stable.sif

-# Generated by CaSQ v0.9.7
+# Generated by CaSQ v0.9.9
 ASC:MAVS:TRAF3_complex_cell POSITIVE ASC:MAVS:TRAF3_complex_cell
 ASC:MAVS_complex POSITIVE ASC:MAVS:TRAF3_complex_cell
 TRAF3 POSITIVE ASC:MAVS:TRAF3_complex_cell

Executable Modules/SBML_qual_build/sif/NLRP3_Activation_stable_raw.sif

-# Generated by CaSQ v0.9.7
+# Generated by CaSQ v0.9.9
 csa29 POSITIVE csa27
 csa28 POSITIVE csa29
 sa99 POSITIVE csa29

Executable Modules/SBML_qual_build/sif/Nsp4_Nsp6_stable.sif

-# Generated by CaSQ v0.9.7
+# Generated by CaSQ v0.9.9
 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 v0.9.7
+# Generated by CaSQ v0.9.9
 csa39 POSITIVE sa164
 sa162 POSITIVE csa39
 sa48 POSITIVE csa39

Executable Modules/SBML_qual_build/sif/Nsp9_protein_stable.sif

-# Generated by CaSQ v0.9.7
+# Generated by CaSQ v0.9.9
 Nsp9_cell POSITIVE Fibrillincomp_complex
 Nsp9_cell POSITIVE Nuclear_Pore_comp_complex
 Nsp9_cell POSITIVE mibcomp_complex

Executable Modules/SBML_qual_build/sif/Nsp9_protein_stable_raw.sif

-# Generated by CaSQ v0.9.7
+# Generated by CaSQ v0.9.9
 a7c94 POSITIVE csa17
 a7c94 POSITIVE csa21
 a7c94 POSITIVE csa28

Executable Modules/SBML_qual_build/sif/Orf10_Cul2_pathway_stable.sif

-# Generated by CaSQ v0.9.7
+# Generated by CaSQ v0.9.9
 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_cell

Executable Modules/SBML_qual_build/sif/Orf10_Cul2_pathway_stable_raw.sif

-# Generated by CaSQ v0.9.7
+# Generated by CaSQ v0.9.9
 csa5 POSITIVE csa2
 csa5 POSITIVE csa35
 csa5 POSITIVE csa4

Executable Modules/SBML_qual_build/sif/Orf3a_stable.sif

-# Generated by CaSQ v0.9.7
+# Generated by CaSQ v0.9.9
 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 v0.9.7
+# Generated by CaSQ v0.9.9
 sa1 POSITIVE csa2
 sa1 POSITIVE csa7
 sa1 POSITIVE sa3

Executable Modules/SBML_qual_build/sif/PAMP_signaling_stable.sif

-# Generated by CaSQ v0.9.7
+# Generated by CaSQ v0.9.9
 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 v0.9.7
+# Generated by CaSQ v0.9.9
 csa56 POSITIVE sa255
 csa56 POSITIVE sa337
 sa77 POSITIVE csa56

Executable Modules/SBML_qual_build/sif/Pyrimidine_deprivation_stable.sif

-# Generated by CaSQ v0.9.7
+# Generated by CaSQ v0.9.9
 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 v0.9.7
+# Generated by CaSQ v0.9.9
 csa8 POSITIVE sa88
 csa8 POSITIVE sa89
 csa19 POSITIVE csa8

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

-# Generated by CaSQ v0.9.7
+# Generated by CaSQ v0.9.9
 Replication_space_transcription_space_complex_space__complex_double_membrane_vesicle_viral_factory POSITIVE CoV_space_poly-br_merase_space_complex_complex_double_membrane_vesicle_viral_factory
 Replication_space_transcription_space_complex_space__complex_double_membrane_vesicle_viral_factory POSITIVE complex_complex_double_membrane_vesicle_viral_factory
 Replication_space_transcription_space_complex_space__complex_double_membrane_vesicle_viral_factory POSITIVE (+)gRNA_space_(including_space_ORF1a_space_ORF1b)_gene_double_membrane_vesicle_viral_factory
@@ -6,35 +6,35 @@ Replication_space_transcription_space_complex_space__complex_double_membrane_ves
 Replication_space_transcription_space_complex_space__complex_double_membrane_vesicle_viral_factory POSITIVE (-)gRNA_space_(including_space_ORF1a_space_ORF1b)_gene
 Replication_space_transcription_space_complex_space__complex_double_membrane_vesicle_viral_factory POSITIVE Replication_space_transcription_space_complex_space__complex_double_membrane_vesicle_viral_factory
 Replication_space_transcription_space_complex_space__complex_double_membrane_vesicle_viral_factory POSITIVE (+)sgRNA_space_(2-9)_gene
-CoV_space_poly-br_merase_space_complex_complex_human_host POSITIVE Replication_space_transcription_space_complex_space__complex_double_membrane_vesicle_viral_factory
-nsp9_human_host POSITIVE Replication_space_transcription_space_complex_space__complex_double_membrane_vesicle_viral_factory
-complex_complex_human_host POSITIVE Replication_space_transcription_space_complex_space__complex_double_membrane_vesicle_viral_factory
-(+)gRNA_space_(including_space_ORF1a_space_ORF1b)_gene_human_host POSITIVE Replication_space_transcription_space_complex_space__complex_double_membrane_vesicle_viral_factory
-(+)gRNA_space_(including_space_ORF1a_space_ORF1b)_gene_human_host POSITIVE pp1ab_human_host
-(+)gRNA_space_(including_space_ORF1a_space_ORF1b)_gene_human_host POSITIVE pp1a_human_host
-nsp8_space_(I) POSITIVE complex_complex_human_host
-nsp8_space_(II) POSITIVE complex_complex_human_host
-nsp7 POSITIVE complex_complex_human_host
-nsp14 POSITIVE CoV_space_poly-br_merase_space_complex_complex_human_host
-nsp10 POSITIVE CoV_space_poly-br_merase_space_complex_complex_human_host
-nsp12 POSITIVE CoV_space_poly-br_merase_space_complex_complex_human_host
-pp1a_human_host POSITIVE nsp2
-pp1a_human_host POSITIVE nsp5
-pp1a_human_host POSITIVE nsp3
-pp1a_human_host POSITIVE nsp4
-pp1a_human_host POSITIVE nsp9_human_host
-pp1a_human_host POSITIVE nsp8_space_(I)
-pp1a_human_host POSITIVE nsp1
-pp1a_human_host POSITIVE nsp7
-pp1a_human_host POSITIVE nsp10
-pp1a_human_host POSITIVE nsp11
-pp1a_human_host POSITIVE nsp8_space_(II)
-pp1a_human_host POSITIVE nsp6
-pp1ab_human_host POSITIVE nsp14
-pp1ab_human_host POSITIVE nsp15
-pp1ab_human_host POSITIVE nsp16
-pp1ab_human_host POSITIVE nsp12
-pp1ab_human_host POSITIVE nsp13
+CoV_space_poly-br_merase_space_complex_complex_cell POSITIVE Replication_space_transcription_space_complex_space__complex_double_membrane_vesicle_viral_factory
+nsp9_cell POSITIVE Replication_space_transcription_space_complex_space__complex_double_membrane_vesicle_viral_factory
+complex_complex_cell POSITIVE Replication_space_transcription_space_complex_space__complex_double_membrane_vesicle_viral_factory
+(+)gRNA_space_(including_space_ORF1a_space_ORF1b)_gene_cell POSITIVE Replication_space_transcription_space_complex_space__complex_double_membrane_vesicle_viral_factory
+(+)gRNA_space_(including_space_ORF1a_space_ORF1b)_gene_cell POSITIVE pp1ab_cell
+(+)gRNA_space_(including_space_ORF1a_space_ORF1b)_gene_cell POSITIVE pp1a_cell
+nsp8_space_(I) POSITIVE complex_complex_cell
+nsp8_space_(II) POSITIVE complex_complex_cell
+nsp7 POSITIVE complex_complex_cell
+nsp14 POSITIVE CoV_space_poly-br_merase_space_complex_complex_cell
+nsp10 POSITIVE CoV_space_poly-br_merase_space_complex_complex_cell
+nsp12 POSITIVE CoV_space_poly-br_merase_space_complex_complex_cell
+pp1a_cell POSITIVE nsp2
+pp1a_cell POSITIVE nsp5
+pp1a_cell POSITIVE nsp3
+pp1a_cell POSITIVE nsp4
+pp1a_cell POSITIVE nsp9_cell
+pp1a_cell POSITIVE nsp8_space_(I)
+pp1a_cell POSITIVE nsp1
+pp1a_cell POSITIVE nsp7
+pp1a_cell POSITIVE nsp10
+pp1a_cell POSITIVE nsp11
+pp1a_cell POSITIVE nsp8_space_(II)
+pp1a_cell POSITIVE nsp6
+pp1ab_cell POSITIVE nsp14
+pp1ab_cell POSITIVE nsp15
+pp1ab_cell POSITIVE nsp16
+pp1ab_cell POSITIVE nsp12
+pp1ab_cell POSITIVE nsp13
 (+)gRNA_space_(including_space_ORF1a_space_ORF1b)_gene_double_membrane_vesicle_viral_factory POSITIVE pp1a_double_membrane_vesicle_viral_factory
 (+)gRNA_space_(including_space_ORF1a_space_ORF1b)_gene_double_membrane_vesicle_viral_factory POSITIVE pp1ab_double_membrane_vesicle_viral_factory
 (+)sgRNA_space_(2-9)_gene POSITIVE viral_space_accessory

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

-# Generated by CaSQ v0.9.7
+# Generated by CaSQ v0.9.9
 glyph2 POSITIVE glyph4
 glyph2 POSITIVE glyph6
 glyph2 POSITIVE glyph17

Executable Modules/SBML_qual_build/sif/Renin_angiotensin_stable.sif

-# Generated by CaSQ v0.9.7
+# Generated by CaSQ v0.9.9
 AGTR1_cell POSITIVE ACE2:AGTR1_complex
 AGTR1_cell POSITIVE AGTR1_cell_active
 ACE2_cell POSITIVE ACE2:AGTR1_complex

Executable Modules/SBML_qual_build/sif/Renin_angiotensin_stable_raw.sif

-# Generated by CaSQ v0.9.7
+# Generated by CaSQ v0.9.9
 sa26 POSITIVE csa4
 sa26 POSITIVE sa102
 sa30 POSITIVE csa4

Executable Modules/SBML_qual_build/sif/TGFB_pathway_stable.sif

-# Generated by CaSQ v0.9.7
+# Generated by CaSQ v0.9.9
 SMAD1/5/8_complex POSITIVE Modulation_of_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 v0.9.7
+# Generated by CaSQ v0.9.9
 csa3 POSITIVE sa55
 sa33 NEGATIVE csa3
 sa33 NEGATIVE csa5

Executable Modules/SBML_qual_build/sif/Virus_replication_cycle_stable.sif

-# Generated by CaSQ v0.9.7
+# Generated by CaSQ v0.9.9
 ACE2:SPIKE_complex_complex_epithelial_cell POSITIVE Nucleocapsid_complex_SARS-CoV-2_virion
 ACE2_epithelial_cell POSITIVE ACE2:SPIKE_complex_complex_epithelial_cell
 S_SARS-CoV-2_virion POSITIVE ACE2:SPIKE_complex_complex_epithelial_cell

Executable Modules/SBML_qual_build/sif/Virus_replication_cycle_stable_raw.sif

-# Generated by CaSQ v0.9.7
+# Generated by CaSQ v0.9.9
 csa430 POSITIVE csa357
 sa1462 POSITIVE csa430
 sa1859 POSITIVE csa430