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

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

-# Generated by CaSQ v0.8.6
+# Generated by CaSQ v0.9.2
 csa11 POSITIVE sa250
 csa11 POSITIVE sa251
 csa11 POSITIVE sa402
@@ -10,20 +10,20 @@ sa167 POSITIVE sa251
 sa169 POSITIVE csa11
 csa13 POSITIVE sa203
 sa177 POSITIVE csa13
-sa177 POSITIVE sa178
+sa177 POSITIVE sa171
 sa175 POSITIVE csa13
 sa175 POSITIVE csa12
-sa175 POSITIVE sa178
+sa175 POSITIVE sa171
 sa202 NEGATIVE csa13
 sa202 POSITIVE csa14
-sa202 NEGATIVE sa178
+sa202 NEGATIVE sa171
 sa202 NEGATIVE sa181
 sa200 POSITIVE csa13
 csa25 NEGATIVE csa13
 csa25 NEGATIVE sa395
 sa205 NEGATIVE csa13
+sa205 NEGATIVE sa171
 sa205 NEGATIVE sa180
-sa205 NEGATIVE sa183
 sa205 NEGATIVE sa213
 sa180 POSITIVE csa12
 sa224 POSITIVE csa16
@@ -31,24 +31,40 @@ sa224 NEGATIVE sa213
 sa224 NEGATIVE sa236
 sa225 POSITIVE csa16
 sa225 POSITIVE sa213
-sa499 POSITIVE csa16
-sa499 POSITIVE csa17
-sa499 NEGATIVE sa202
-sa499 POSITIVE sa210
-sa499 POSITIVE sa301
-sa499 POSITIVE sa395
-sa499 POSITIVE sa411
+sa207 POSITIVE csa16
+sa207 POSITIVE csa17
+sa207 POSITIVE csa14
+sa207 POSITIVE csa32
+sa207 POSITIVE csa38
+sa207 POSITIVE sa179
+sa207 POSITIVE sa194
+sa207 NEGATIVE sa202
+sa207 POSITIVE sa205
+sa207 POSITIVE sa210
+sa207 POSITIVE sa238
+sa207 POSITIVE sa242
+sa207 POSITIVE sa244
+sa207 POSITIVE sa253
+sa207 POSITIVE sa301
+sa207 POSITIVE sa304
+sa207 POSITIVE sa306
+sa207 POSITIVE sa387
+sa207 NEGATIVE sa394
+sa207 POSITIVE sa395
+sa207 POSITIVE sa410
+sa207 POSITIVE sa411
+sa207 POSITIVE sa459
+sa207 POSITIVE sa503
+sa207 POSITIVE sa531
 csa17 POSITIVE csa42
 csa17 POSITIVE sa395
 sa181 POSITIVE csa14
 sa181 POSITIVE csa25
+sa181 POSITIVE sa171
 sa181 POSITIVE sa172
 sa181 POSITIVE sa173
 sa181 POSITIVE sa180
-sa181 POSITIVE sa183
 sa181 POSITIVE sa227
-sa481 POSITIVE csa14
-sa481 POSITIVE csa38
 sa301 POSITIVE csa25
 csa27 POSITIVE csa32
 csa27 POSITIVE sa253
@@ -60,16 +76,6 @@ csa32 POSITIVE csa43
 csa32 POSITIVE sa211
 csa32 POSITIVE sa271
 csa32 POSITIVE sa390
-sa207 POSITIVE csa32
-sa207 POSITIVE sa179
-sa207 POSITIVE sa205
-sa207 POSITIVE sa238
-sa207 POSITIVE sa242
-sa207 POSITIVE sa244
-sa207 POSITIVE sa253
-sa207 POSITIVE sa304
-sa207 POSITIVE sa306
-sa207 POSITIVE sa410
 sa314 POSITIVE csa32
 sa314 POSITIVE sa253
 csa35 POSITIVE csa32
@@ -87,6 +93,7 @@ sa391 POSITIVE csa43
 sa391 POSITIVE sa387
 sa212 POSITIVE csa38
 sa212 POSITIVE sa210
+sa212 POSITIVE sa253
 sa412 POSITIVE csa38
 csa42 POSITIVE sa430
 sa431 POSITIVE csa42
@@ -101,12 +108,19 @@ sa165 POSITIVE sa173
 sa165 POSITIVE sa251
 sa170 POSITIVE sa165
 sa170 POSITIVE sa171
+sa179 POSITIVE sa171
+sa179 POSITIVE sa180
+sa402 POSITIVE sa171
+sa402 POSITIVE sa213
+sa402 POSITIVE sa407
+sa198 POSITIVE sa171
+sa198 POSITIVE sa194
+sa198 POSITIVE sa407
 sa173 POSITIVE sa175
 sa173 POSITIVE sa212
 sa174 POSITIVE sa175
-sa179 POSITIVE sa180
-sa179 POSITIVE sa183
 sa203 POSITIVE sa181
+sa203 POSITIVE sa395
 sa355 POSITIVE sa181
 sa194 POSITIVE sa213
 sa194 POSITIVE sa224
@@ -115,16 +129,7 @@ sa194 POSITIVE sa400
 sa194 POSITIVE sa484
 sa194 POSITIVE sa503
 sa194 POSITIVE sa519
-sa480 POSITIVE sa194
-sa480 POSITIVE sa387
-sa480 NEGATIVE sa394
-sa480 POSITIVE sa459
-sa480 POSITIVE sa503
-sa480 POSITIVE sa531
 sa195 POSITIVE sa194
-sa198 POSITIVE sa194
-sa198 POSITIVE sa397
-sa198 POSITIVE sa407
 sa196 POSITIVE sa195
 sa197 POSITIVE sa195
 sa415 POSITIVE sa197
@@ -139,9 +144,6 @@ sa227 POSITIVE sa210
 sa211 POSITIVE sa212
 sa213 POSITIVE sa212
 sa236 POSITIVE sa212
-sa402 POSITIVE sa213
-sa402 POSITIVE sa397
-sa402 POSITIVE sa407
 sa400 NEGATIVE sa213
 sa400 NEGATIVE sa224
 sa400 POSITIVE sa483
@@ -158,7 +160,6 @@ sa416 POSITIVE sa244
 sa416 POSITIVE sa304
 sa416 POSITIVE sa306
 sa244 POSITIVE sa271
-sa468 POSITIVE sa253
 sa387 POSITIVE sa271
 sa387 POSITIVE sa388
 sa410 POSITIVE sa271
@@ -182,7 +183,6 @@ sa390 POSITIVE sa408
 sa390 POSITIVE sa409
 sa394 POSITIVE sa400
 sa395 POSITIVE sa424
-sa498 POSITIVE sa395
 sa425 POSITIVE sa424
 sa430 POSITIVE sa441
 sa484 POSITIVE sa441

Executable Modules/SBML_qual_build/sif/ER_Stress_stable.sif

-# Generated by CaSQ v0.8.6
+# Generated by CaSQ v0.9.2
 EIF2-P:GDP_complex POSITIVE ATF4_rna
 EIF2S1_phosphorylated POSITIVE EIF2-P:GDP_complex
 EIF2S1_phosphorylated POSITIVE EIF2S1
@@ -6,12 +6,14 @@ EIF2S2 POSITIVE EIF2-P:GDP_complex
 EIF2S2 POSITIVE EIF2:GDP_complex
 EIF2S3:GDP_complex POSITIVE EIF2-P:GDP_complex
 EIF2S3:GDP_complex POSITIVE EIF2:GDP_complex
+TRAF2:ERN1_complex POSITIVE TRAF2
 TRAF2:ERN1_complex POSITIVE UPR_phenotype
-TRAF2:ERN1_complex POSITIVE TRAF2_Cytoplasm
 TRAF2:ERN1_complex POSITIVE XBP1_rna
 TRAF2:ERN1_complex POSITIVE MAP3K5_phosphorylated
 ERN1:Unfolded_space_protein_complex POSITIVE TRAF2:ERN1_complex
-TRAF2_Cytoplasm POSITIVE TRAF2:ERN1_complex
+TRAF2 POSITIVE TRAF2:ERN1_complex
+TRAF2 POSITIVE TRAF2
+TRAF2 POSITIVE MAP3K5_phosphorylated
 BAK1:ERN1_complex POSITIVE TRAF2:ERN1_complex
 BAX:ERN1_complex POSITIVE TRAF2:ERN1_complex
 BCL2 NEGATIVE TRAF2:ERN1_complex
@@ -37,14 +39,14 @@ Ca2+space_ER_space_depletion_phenotype POSITIVE SIGMAR1:ITPR3_complex
 Ca2+space_ER_space_depletion_phenotype POSITIVE HSPA5_Endoplasmic_Reticulum
 Ca2+space_ER_space_depletion_phenotype POSITIVE SIGMAR1_MAM_(mito-associated_ER_membrane)
 EIF2:GDP:Met-tRNA_complex POSITIVE Ternary_space_Complex_complex
-EIF2:GDP:Met-tRNA_complex POSITIVE GDP_simple_molecule_Cytoplasm
+EIF2:GDP:Met-tRNA_complex POSITIVE GDP_simple_molecule
 Met-tRNA_rna POSITIVE EIF2:GDP:Met-tRNA_complex
 EIF2:GDP_complex POSITIVE EIF2:GDP:Met-tRNA_complex
 Ternary_space_Complex_complex POSITIVE EIF2:GDP:Met-tRNA_complex
-Ternary_space_Complex_complex POSITIVE GTP_simple_molecule_Cytoplasm
+Ternary_space_Complex_complex POSITIVE GTP_simple_molecule
 Ternary_space_Complex_complex POSITIVE Translation_space_initiation_phenotype
-GDP_simple_molecule_Cytoplasm POSITIVE EIF2:GDP:Met-tRNA_complex
-GDP_simple_molecule_Cytoplasm POSITIVE GTP_simple_molecule_Cytoplasm
+GDP_simple_molecule POSITIVE EIF2:GDP:Met-tRNA_complex
+GDP_simple_molecule POSITIVE GTP_simple_molecule
 CASP8:FADD:MAP1LC3A:SQSTM1:ATG5_complex POSITIVE Apoptosis_phenotype_Cytoplasm
 CASP8:CASP8-ubq:FADD_complex POSITIVE CASP8:FADD:MAP1LC3A:SQSTM1:ATG5_complex
 SQSTM1_space_ POSITIVE CASP8:FADD:MAP1LC3A:SQSTM1:ATG5_complex
@@ -52,12 +54,16 @@ MAP1LC3A POSITIVE CASP8:FADD:MAP1LC3A:SQSTM1:ATG5_complex
 ATG5 POSITIVE CASP8:FADD:MAP1LC3A:SQSTM1:ATG5_complex
 TRIM13 POSITIVE CASP8:FADD:MAP1LC3A:SQSTM1:ATG5_complex
 ERN1_Endoplasmic_Reticulum POSITIVE ERN1:Unfolded_space_protein_complex
-Unfolded_space_protein_Endoplasmic_Reticulum POSITIVE ERN1:Unfolded_space_protein_complex
+Unfolded_space_protein POSITIVE ERN1:Unfolded_space_protein_complex
+Unfolded_space_protein POSITIVE EIF2AK3:EIF2AK3_complex
+Unfolded_space_protein POSITIVE HSPA5_Endoplasmic_Reticulum
+Unfolded_space_protein POSITIVE ATF6_Endoplasmic_Reticulum
+Unfolded_space_protein POSITIVE accumulation_space_of_space_misfolded_space_protein_space_in_space_ER_phenotype
 SIGMAR1:HSPA5_complex POSITIVE HSPA5_Endoplasmic_Reticulum
 SIGMAR1:HSPA5_complex POSITIVE SIGMAR1_MAM_(mito-associated_ER_membrane)
+SIGMAR1_Endoplasmic_Reticulum POSITIVE SIGMAR1:HSPA5_complex
 HSPA5_Endoplasmic_Reticulum POSITIVE SIGMAR1:HSPA5_complex
 HSPA5_Endoplasmic_Reticulum POSITIVE endoplasmic_space_reticulum_space_calcium_space_ion_space_homeostasis_phenotype
-SIGMAR1_Endoplasmic_Reticulum POSITIVE SIGMAR1:HSPA5_complex
 VAPB:RMDN3_complex POSITIVE mitochondrion-endoplasmic_space_reticulum_space_membrane_space_tethering_space__phenotype
 VAPB POSITIVE VAPB:RMDN3_complex
 VAPB POSITIVE Ca2+space_mitochondrial_space_concentration_phenotype
@@ -67,10 +73,10 @@ RMDN3 POSITIVE VAPB:RMDN3_complex
 RMDN3 POSITIVE Ca2+space_mitochondrial_space_concentration_phenotype
 RMDN3 NEGATIVE autophagy_phenotype
 RMDN3 NEGATIVE Ca2+space_cytosolic_space_concentration_phenotype
-GTP_simple_molecule_Cytoplasm POSITIVE Ternary_space_Complex_complex
-GTP_simple_molecule_Cytoplasm POSITIVE GDP_simple_molecule_Cytoplasm
+GTP_simple_molecule POSITIVE Ternary_space_Complex_complex
+GTP_simple_molecule POSITIVE GDP_simple_molecule
 EIF2B_complex POSITIVE Ternary_space_Complex_complex
-EIF2B_complex POSITIVE GDP_simple_molecule_Cytoplasm
+EIF2B_complex POSITIVE GDP_simple_molecule