Merge branch 'repo_update' into 'master'

NLRP3 v3

See merge request !262

Executable Modules/SBML_qual_build/sif/Apoptosis_stable.sif

-# Generated by CaSQ v0.8.6
+# Generated by CaSQ v0.9.2
 FAS/FASL_complex POSITIVE FADD
 BAD/BBC3/BCL2L11_complex POSITIVE BAX
 BCL2/MCL1/BCL2L1_complex POSITIVE BAD/BBC3/BCL2L11_complex
 BCL2/MCL1/BCL2L1_complex NEGATIVE BAX
-Apoptosome_complex POSITIVE CASP9_Cytoplasm
+Apoptosome_complex POSITIVE CASP9
 CYCS POSITIVE Apoptosome_complex
 APAF1 POSITIVE Apoptosome_complex
-CASP9_Cytoplasm POSITIVE Apoptosome_complex
+CASP9 POSITIVE Apoptosome_complex
+CASP9 POSITIVE CASP3
+CASP9 POSITIVE CASP9
+CASP9 POSITIVE CASP7
 AKT1 NEGATIVE Apoptosome_complex
-AKT1 NEGATIVE CASP9_Cytoplasm
+AKT1 NEGATIVE CASP9
+AKT1 POSITIVE AKT1
 AKT1 NEGATIVE BAD
 TNF/TNFRSF1A_complex POSITIVE TRADD/FADD_complex
 TRADD/FADD_complex POSITIVE CASP8
+TRADD POSITIVE TRADD/FADD_complex
 FADD POSITIVE TRADD/FADD_complex
+FADD POSITIVE FADD
 FADD POSITIVE CASP8
-TRADD POSITIVE TRADD/FADD_complex
 Orf7a POSITIVE BCL2/MCL1/BCL2L1_complex
 E POSITIVE BCL2/MCL1/BCL2L1_complex
 BAD NEGATIVE BCL2/MCL1/BCL2L1_complex
+BAD POSITIVE BAD
+CASP8 POSITIVE CASP8
 CASP8 POSITIVE CASP3
 CASP8 POSITIVE BID
 CASP8 POSITIVE CASP7
+CASP3 POSITIVE CASP3
 CASP3 POSITIVE Apoptosis_phenotype
-CASP9_Cytoplasm POSITIVE CASP3
-CASP9_Cytoplasm POSITIVE CASP7
+BID POSITIVE BID
 BID POSITIVE BAX
 MAPK14 POSITIVE CYCS
+MAPK14 POSITIVE MAPK14
 M NEGATIVE AKT1
+BAX POSITIVE BAX
+CASP7 POSITIVE CASP7
 CASP7 POSITIVE Apoptosis_phenotype
 Orf3b POSITIVE Apoptosis_phenotype
 Orf8a POSITIVE Apoptosis_phenotype

Executable Modules/SBML_qual_build/sif/Apoptosis_stable_raw.sif

-# Generated by CaSQ v0.8.6
-csa2 POSITIVE sa10
-csa3 POSITIVE sa31
+# Generated by CaSQ v0.9.2
+csa2 POSITIVE sa9
+csa3 POSITIVE sa30
 csa11 POSITIVE csa3
-csa11 NEGATIVE sa31
-csa5 POSITIVE sa19
+csa11 NEGATIVE sa30
+csa5 POSITIVE sa18
 sa25 POSITIVE csa5
 sa27 POSITIVE csa5
-sa47 POSITIVE csa5
-sa29 NEGATIVE csa5
-sa29 NEGATIVE sa19
-sa29 NEGATIVE sa79
+sa18 POSITIVE csa5
+sa18 POSITIVE sa15
+sa18 POSITIVE sa18
+sa18 POSITIVE sa39
+sa28 NEGATIVE csa5
+sa28 NEGATIVE sa18
+sa28 POSITIVE sa28
+sa28 NEGATIVE sa78
 csa1 POSITIVE csa6
-csa6 POSITIVE sa14
-sa10 POSITIVE csa6
-sa10 POSITIVE sa14
+csa6 POSITIVE sa13
 sa44 POSITIVE csa6
+sa9 POSITIVE csa6
+sa9 POSITIVE sa9
+sa9 POSITIVE sa13
 sa43 POSITIVE csa11
 sa69 POSITIVE csa11
-sa79 NEGATIVE csa11
-sa14 POSITIVE sa17
-sa14 POSITIVE sa23
-sa14 POSITIVE sa40
-sa17 POSITIVE sa41
-sa19 POSITIVE sa17
-sa19 POSITIVE sa40
-sa23 POSITIVE sa31
-sa50 POSITIVE sa25
-sa42 NEGATIVE sa29
-sa40 POSITIVE sa41
+sa78 NEGATIVE csa11
+sa78 POSITIVE sa78
+sa13 POSITIVE sa13
+sa13 POSITIVE sa15
+sa13 POSITIVE sa22
+sa13 POSITIVE sa39
+sa15 POSITIVE sa15
+sa15 POSITIVE sa41
+sa22 POSITIVE sa22
+sa22 POSITIVE sa30
+sa49 POSITIVE sa25
+sa49 POSITIVE sa49
+sa42 NEGATIVE sa28
+sa30 POSITIVE sa30
+sa39 POSITIVE sa39
+sa39 POSITIVE sa41
 sa72 POSITIVE sa41
 sa73 POSITIVE sa41
 sa74 POSITIVE sa41
 sa76 POSITIVE sa41
 sa77 POSITIVE sa41
 sa75 POSITIVE sa41
-sa48 POSITIVE sa50
+sa48 POSITIVE sa49

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

-# Generated by CaSQ v0.8.6
+# Generated by CaSQ v0.9.2
 KNG1:KLKB1_complex POSITIVE Kininogen
 KNG1:KLKB1_complex POSITIVE Kallikrein
 KNG1:KLKB1_complex POSITIVE Bradykinin
 KLKB1 POSITIVE KNG1:KLKB1_complex
 KLKB1 POSITIVE F12a
-KLKB1 POSITIVE Small_peptide_Blood
-KLKB1 POSITIVE Plasmin_Blood
+KLKB1 POSITIVE Small_peptide
+KLKB1 POSITIVE Plasmin
 KLKB1 POSITIVE Kallikrein
 KNG1 POSITIVE KNG1:KLKB1_complex
 F5a:F10a_complex POSITIVE Thrombin_Blood
 F10 POSITIVE F5a:F10a_complex
-F10 POSITIVE Small_peptide_Blood
+F10 POSITIVE Small_peptide
 F9a POSITIVE F5a:F10a_complex
 F9a POSITIVE F8:F9_complex
-F9a POSITIVE Small_peptide_Blood
+F9a POSITIVE Small_peptide
 Antithrombin NEGATIVE F5a:F10a_complex
 Antithrombin POSITIVE TAT_complex_complex
-Antithrombin NEGATIVE Small_peptide_Blood
-Antithrombin NEGATIVE Thrombin_Blood
+Antithrombin NEGATIVE Small_peptide
+Antithrombin NEGATIVE Thrombin_Blood_active
 F5 POSITIVE F5a:F10a_complex
 Thrombin:Thrombomodulin_complex NEGATIVE F5a:F10a_complex
 Thrombin:Thrombomodulin_complex NEGATIVE Fibrin_monomer
 PROC NEGATIVE F5a:F10a_complex
+PROC NEGATIVE Small_peptide
 PROC NEGATIVE F8a
-PROC NEGATIVE Small_peptide_Blood
-PROC NEGATIVE PLAT_Blood
+PROC NEGATIVE PLAT_Blood_active
 F8a POSITIVE F8:F9_complex
 SERPINE1 POSITIVE PLAT:SERPINE1_complex
-SERPINE1 NEGATIVE PLAT_Blood
+SERPINE1 NEGATIVE PLAT_Blood_active
 SERPINE1 NEGATIVE PLAU
 PLAT_Blood POSITIVE PLAT:SERPINE1_complex
-PLAT_Blood POSITIVE PLAT_Blood
-SARS-CoV-2_infection_phenotype_Blood POSITIVE PLAT:SERPINE1_complex
-SARS-CoV-2_infection_phenotype_Blood POSITIVE Fibrinogen_complex
-SARS-CoV-2_infection_phenotype_Blood NEGATIVE Antithrombin
-SARS-CoV-2_infection_phenotype_Blood POSITIVE D-dimer
-SARS-CoV-2_infection_phenotype_Blood POSITIVE Thrombomodulin
-SARS-CoV-2_infection_phenotype_Blood POSITIVE Fibrin_monomer
-SARS-CoV-2_infection_phenotype_Blood POSITIVE VWF
+PLAT_Blood POSITIVE PLAT_Blood_active
+SARS-CoV-2_infection_phenotype POSITIVE PLAT:SERPINE1_complex
+SARS-CoV-2_infection_phenotype POSITIVE Fibrinogen_complex
+SARS-CoV-2_infection_phenotype POSITIVE TAT_complex_complex
+SARS-CoV-2_infection_phenotype POSITIVE C5b-9_complex_Endothelium,_vascular
+SARS-CoV-2_infection_phenotype POSITIVE SERPINF2:Plasmin_complex
+SARS-CoV-2_infection_phenotype POSITIVE F8
+SARS-CoV-2_infection_phenotype POSITIVE angiotensin_II_simple_molecule
+SARS-CoV-2_infection_phenotype NEGATIVE Antithrombin
+SARS-CoV-2_infection_phenotype POSITIVE PROC
+SARS-CoV-2_infection_phenotype POSITIVE D-dimer
+SARS-CoV-2_infection_phenotype POSITIVE TNF
+SARS-CoV-2_infection_phenotype POSITIVE IL6
+SARS-CoV-2_infection_phenotype POSITIVE IL1B
+SARS-CoV-2_infection_phenotype POSITIVE C5a
+SARS-CoV-2_infection_phenotype POSITIVE Thrombomodulin
+SARS-CoV-2_infection_phenotype POSITIVE IL8
+SARS-CoV-2_infection_phenotype POSITIVE IL2RA
+SARS-CoV-2_infection_phenotype POSITIVE C4d
+SARS-CoV-2_infection_phenotype NEGATIVE ACE2_Endothelium,_vascular
+SARS-CoV-2_infection_phenotype POSITIVE Fibrin_monomer
+SARS-CoV-2_infection_phenotype POSITIVE CRP
+SARS-CoV-2_infection_phenotype POSITIVE VWF
+SARS-CoV-2_infection_phenotype POSITIVE MASP2
+SARS-CoV-2_infection_phenotype POSITIVE aldosterone_simple_molecule_Blood
+SARS-CoV-2_infection_phenotype POSITIVE Hypokalemia_phenotype
 Fibrinogen_complex POSITIVE Fibrinogen:GP6_complex
 Fibrinogen_complex POSITIVE Fibrin_monomer
-Thrombin_Blood POSITIVE TAT_complex_complex
-Thrombin_Blood POSITIVE Thrombin:Thrombomodulin_complex
-Thrombin_Blood POSITIVE F11
-Thrombin_Blood POSITIVE F11a
-Thrombin_Blood POSITIVE F8a
-Thrombin_Blood POSITIVE Small_peptide_Blood
-Thrombin_Blood POSITIVE TAFI
-SARS-CoV-2_infection_phenotype_Blood POSITIVE TAT_complex_complex
-SARS-CoV-2_infection_phenotype_Blood POSITIVE SERPINF2:Plasmin_complex
+Thrombin_Blood_active POSITIVE TAT_complex_complex
+Thrombin_Blood_active POSITIVE Thrombin:Thrombomodulin_complex
+Thrombin_Blood_active POSITIVE Small_peptide
+Thrombin_Blood_active POSITIVE F11
+Thrombin_Blood_active POSITIVE F11a
+Thrombin_Blood_active POSITIVE F8a
+Thrombin_Blood_active POSITIVE TAFI
 Thrombomodulin POSITIVE Thrombin:Thrombomodulin_complex
 C3b:Bb:C3b_complex POSITIVE C5b-9_complex_Endothelium,_vascular
 C3b:Bb:C3b_complex POSITIVE C5a
@@ -60,16 +76,6 @@ C5b-9_complex_Endothelium,_vascular POSITIVE C5b-9_complex_Endothelium,_vascular
 C5b-9_complex_Endothelium,_vascular POSITIVE Plasminogen
 C5b-9_complex_Endothelium,_vascular POSITIVE Thrombosis_phenotype_Blood
 C5b-9_complex_Endothelium,_vascular POSITIVE C5b-9_deposition_phenotype
-SARS-CoV-2_infection_phenotype_Blood POSITIVE C5b-9_complex_Endothelium,_vascular
-SARS-CoV-2_infection_phenotype_Blood POSITIVE F8
-SARS-CoV-2_infection_phenotype_Blood POSITIVE PROC
-SARS-CoV-2_infection_phenotype_Blood POSITIVE TNF
-SARS-CoV-2_infection_phenotype_Blood POSITIVE IL6
-SARS-CoV-2_infection_phenotype_Blood POSITIVE IL1B
-SARS-CoV-2_infection_phenotype_Blood POSITIVE C5a
-SARS-CoV-2_infection_phenotype_Blood POSITIVE IL8
-SARS-CoV-2_infection_phenotype_Blood POSITIVE IL2RA
-SARS-CoV-2_infection_phenotype_Blood POSITIVE CRP
 C5 POSITIVE C5b-9_complex_Endothelium,_vascular
 C5 POSITIVE C5a
 C2a:C4b_complex POSITIVE C5b-9_complex_Endothelium,_vascular
@@ -85,8 +91,9 @@ ACE2_Blood POSITIVE ACE2_Endothelium,_vascular
 S POSITIVE ACE2:Spike_complex
 S POSITIVE C5b-9_complex_Endothelium,_vascular
 S POSITIVE C4d
-Plasmin_Blood POSITIVE SERPINF2:Plasmin_complex
-Plasmin_Blood POSITIVE D-dimer
+Plasmin POSITIVE SERPINF2:Plasmin_complex
+Plasmin POSITIVE D-dimer
+Plasmin POSITIVE C5a
 SERPINF2 POSITIVE SERPINF2:Plasmin_complex
 Fibrinogen:GP6_complex POSITIVE platelet_activation_phenotype
 GP6 POSITIVE Fibrinogen:GP6_complex
@@ -100,31 +107,29 @@ F12a POSITIVE F11
 F12a POSITIVE F11a
 F12a POSITIVE Kallikrein
 F12 POSITIVE F12a
-F12 POSITIVE Small_peptide_Blood
+F12 POSITIVE Small_peptide
+F8 POSITIVE Small_peptide
+F8 POSITIVE F8a
+Bradykinin POSITIVE Small_peptide
+Bradykinin POSITIVE PLAT_Blood_active
+Bradykinin POSITIVE Bradykinin(1-5)
+ACE POSITIVE Small_peptide
+ACE POSITIVE angiotensin_II_simple_molecule
+ACE POSITIVE Bradykinin(1-5)
 F11a POSITIVE F9a
-F11a POSITIVE Plasmin_Blood
+F11a POSITIVE Plasmin
 F9 POSITIVE F9a
-F8 POSITIVE F8a
-F8 POSITIVE Small_peptide_Blood
-Thrombin_Blood POSITIVE Thrombin_Blood
-Heparin_simple_molecule POSITIVE Thrombin_Blood
-angiotensin_II_simple_molecule POSITIVE PLAT_Blood
+Thrombin_Blood POSITIVE Thrombin_Blood_active
+Thrombin_Blood POSITIVE Fibrin_monomer
+Heparin_simple_molecule POSITIVE Thrombin_Blood_active
+angiotensin_II_simple_molecule POSITIVE PLAT_Blood_active
 angiotensin_II_simple_molecule POSITIVE SERPINE1
 angiotensin_II_simple_molecule POSITIVE Thrombosis_phenotype_Blood
 angiotensin_II_simple_molecule POSITIVE angiotensin_I-7_simple_molecule
 angiotensin_II_simple_molecule POSITIVE AGTR1_Platelet
 angiotensin_II_simple_molecule POSITIVE aldosterone_simple_molecule_Blood
 angiotensin_II_simple_molecule POSITIVE AGTR1_Endothelium,_vascular
-SARS-CoV-2_infection_phenotype_Blood POSITIVE angiotensin_II_simple_molecule
-SARS-CoV-2_infection_phenotype_Blood POSITIVE C4d
-SARS-CoV-2_infection_phenotype_Blood NEGATIVE ACE2_Endothelium,_vascular
-SARS-CoV-2_infection_phenotype_Blood POSITIVE MASP2
-SARS-CoV-2_infection_phenotype_Blood POSITIVE aldosterone_simple_molecule_Blood
-SARS-CoV-2_infection_phenotype_Blood POSITIVE Hypokalemia_phenotype
 angiotensin_I_simple_molecule POSITIVE angiotensin_II_simple_molecule
-ACE POSITIVE angiotensin_II_simple_molecule
-ACE POSITIVE Small_peptide_Blood
-ACE POSITIVE Bradykinin(1-5)
 AGT POSITIVE angiotensin_I_simple_molecule
 REN POSITIVE angiotensin_I_simple_molecule
 Prorenin POSITIVE REN
@@ -136,13 +141,10 @@ aldosterone_simple_molecule_Blood POSITIVE Hypokalemia_phenotype
 Prothrombin POSITIVE Thrombin_Blood
 Fibrin_polymer POSITIVE D-dimer
 TAFI POSITIVE D-dimer
-Plasminogen POSITIVE Plasmin_Blood
-PLAT_Blood POSITIVE Plasmin_Blood
-PLAU POSITIVE Plasmin_Blood
-Bradykinin POSITIVE PLAT_Blood
-Bradykinin POSITIVE Small_peptide_Blood
-Bradykinin POSITIVE Bradykinin(1-5)
-angiotensin_I-7_simple_molecule NEGATIVE PLAT_Blood
+Plasminogen POSITIVE Plasmin
+PLAT_Blood_active POSITIVE Plasmin
+PLAU POSITIVE Plasmin
+angiotensin_I-7_simple_molecule NEGATIVE PLAT_Blood_active
 angiotensin_I-7_simple_molecule NEGATIVE SERPINE1
 angiotensin_I-7_simple_molecule POSITIVE MAS1
 IL6 POSITIVE SERPINE1
@@ -158,7 +160,6 @@ cytokine_storm_phenotype POSITIVE IL1B
 cytokine_storm_phenotype POSITIVE IL8
 cytokine_storm_phenotype POSITIVE IL2RA
 IL1B POSITIVE Thrombosis_phenotype_Blood
-Plasmin_Blood POSITIVE C5a
 C4d POSITIVE Thrombosis_phenotype_Blood
 C4d POSITIVE C4d_deposition_phenotype
 CRP POSITIVE Thrombosis_phenotype_Blood
@@ -182,7 +183,6 @@ C5b-9_deposition_phenotype POSITIVE apoptosis_phenotype
 C5b-9_deposition_phenotype POSITIVE platelet_aggregation_phenotype
 ACE2_Endothelium,_vascular POSITIVE angiotensin_I-7_simple_molecule
 Fibrin_monomer POSITIVE Fibrin_polymer
-Thrombin_Blood POSITIVE Fibrin_monomer
 F13a POSITIVE Fibrin_polymer
 platelet_activation_phenotype POSITIVE thrombus_formation_phenotype
 AGTR1_Platelet POSITIVE thrombus_formation_phenotype