Test changes to contact-inhibition-hippo-yap

Examples/biology/contactinhibitionhippoyap/contact-inhibition-hippo-yap.bngl

@@ -30,6 +30,7 @@ begin parameters
     YAP_tot 500
     TEAD_tot 150
     NF2_tot 100
+    Contact_total 1000
     k_contact_pulse 1.0      # Density-dependent activation triggernal rate
 end parameters
 
@@ -42,7 +43,7 @@ begin molecule types
 end molecule types
 
 begin seed species
-    Contact(s~low) 1000
+    Contact(s~low) Contact_total
     MST(s~U) MST_tot
     LATS(s~U) LATS_tot
     YAP(b,s~U,loc~cyt) YAP_tot

Examples/biology/contactinhibitionhippoyap/metadata.yaml

@@ -1,24 +1,57 @@
 id: "contact-inhibition-hippo-yap"
 name: "contact inhibition hippo yap"
 description: "Hippo Pathway: Contact inhibition and YAP regulation."
+
 contributors:
   - name: "Achyudhan"
+  - name: "Nabil Mardhy"
+
 tags: ["contact", "inhibition", "hippo", "yap", "mst", "lats", "tead"]
+
+date:
+  last_tested: 2026-07-02
+
 category: "signaling"
+biol_categories: ["signaling"]
+comp_categories: ["other"]
+
 compatibility:
+  rr_compatible: true
+  bnglviz_compatible: true
   bng2_compatible: true
-  simulation_methods: ["ode"]
+  bngp_compatible: true
+  vcell_compatible: true
+  vcell_errors: "to run put actions outside of model"
+  simulation_methods: ["ode", "ssa"]
+  nfsim_compatible: true
+  molclustpy_compatible: true
   uses_compartments: false
   uses_energy: false
   uses_functions: true
-  nfsim_compatible: false
+
+
+features:
+  uses_generate_network: true
+  default_sim_command: "ode" 
+  uses_energy: false
+  uses_functions: true
+  uses_totalrate: false
+  uses_moveconnected: false
+  uses_trash_molecules: false
+  uses_anchors: false
+  uses_multiple_identical_sites: false
+  uses_deletes_molecules: false
+  uses_exclude_include_reactants: false
+
 source:
   origin: "ai-generated"
   original_format: "bngl"
   original_repository: "bionetgen-web-simulator"
   source_path: "example-models/contact-inhibition-hippo-yap.bngl"
+
 playground:
   visible: false
   gallery_categories: ["test-models"]
   featured: false
   difficulty: "advanced"
+

Examples/biology/ire1axbp1erstress/ire1a-xbp1-er-stress.bngl

@@ -27,28 +27,29 @@ begin parameters
     XBP1_mRNA 1000     # The splicing substrate
     Target_mRNA 800    # RIDD substrate
     BiP_tot 300
+    Unfolded_tot 10
 end parameters
 
 begin molecule types
     IRE1(b,s~U~P)
     BiP(b)
     Unfolded(b)
     XBP1(s~u~s)        # u: unspliced,s: spliced
-    RIDD_Target()      # Vulnerable mRNA pool
+    RIDD_Target(s)      # Vulnerable mRNA pool
 end molecule types
 
 begin seed species
     IRE1(b,s~U) IRE1_tot
     BiP(b) BiP_tot
-    Unfolded(b) 10
+    Unfolded(b) Unfolded_tot
     XBP1(s~u) XBP1_mRNA
-    RIDD_Target() Target_mRNA
+    RIDD_Target(s) Target_mRNA
 end seed species
 
 begin observables
     # KEY BIOLOGICAL OUTPUTS
     Molecules ProSurvival_XBP1 XBP1(s~s)                # Adaptive output
-    Molecules RIDD_Drive       RIDD_Target()            # Destructive output (mRNA decay)
+    Molecules RIDD_Drive       RIDD_Target(s)            # Destructive output (mRNA decay)
     Molecules Active_IRE1      IRE1(s~P)                # Signaling sensor status
     Molecules Stress_Burden    Unfolded()              # Unbuffered protein load
     Molecules Chaperone_Bip   BiP()                    # ER capacity index
@@ -77,7 +78,7 @@ begin reaction rules
     IRE1(s~P) + XBP1(s~u) -> IRE1(s~P) + XBP1(s~s) k_xbp1_splice
 
     # RIDD: Active IRE1 degrades target mRNAs (Functional Rate)
-    RIDD_Target() -> 0 v_ridd()
+    RIDD_Target(s) -> 0 v_ridd()
 
     ## ADAPTATION Stage
     # Spliced XBP1 induces BiP (Hill-driven burst)
@@ -90,7 +91,7 @@ begin reaction rules
     ## RESET Phase
     IRE1(s~P) -> IRE1(s~U) k_reset
     XBP1(s~s) -> 0 0.05
-    0 -> RIDD_Target() 0.1
+    0 -> RIDD_Target(s) 0.1
 end reaction rules
 
 begin actions

Examples/biology/ire1axbp1erstress/metadata.yaml

@@ -1,24 +1,61 @@
 id: "ire1a-xbp1-er-stress"
 name: "ire1a xbp1 er stress"
 description: "IRE1a/XBP1 ER Stress: Chaperone buffering and mRNA decay (RIDD)."
+
 contributors:
   - name: "Achyudhan"
+  - name: "Nabil Mardhy"
+
 tags: ["ire1a", "xbp1", "er", "stress", "ire1", "bip", "unfolded", "ridd_target"]
+date:
+  last_tested: 2026-07-07
+
 category: "signaling"
+
+biol_categories: ["signaling"]
+
+comp_categories: ["other"]
+
 compatibility:
+  rr_compatible: true
+  bnglviz_compatible: true
   bng2_compatible: true
-  simulation_methods: ["ode"]
+  bngp_compatible: true
+  vcell_compatible: false
+  vcell_errors: "Encountered -> at line 69"
+  simulation_methods: ["ode", "ssa"]
+  molclustpy_compatible: true
+  uses_energy: false
+  uses_functions: true
   uses_compartments: false
+  nfsim_compatible: true
+
+features:
+  uses_generate_network: true
+  default_sim_command: "ode" 
+  uses_totalrate: false
+  uses_moveconnected: false
+  uses_trash_molecules: false
+  uses_anchors: false
+  uses_multiple_identical_sites: false
+  uses_deletes_molecules: true
+  uses_exclude_include_reactants: false
   uses_energy: false
   uses_functions: true
-  nfsim_compatible: false
+  uses_compartments: false
+
 source:
   origin: "ai-generated"
   original_format: "bngl"
   original_repository: "bionetgen-web-simulator"
   source_path: "example-models/ire1a-xbp1-er-stress.bngl"
+
 playground:
   visible: false
   gallery_categories: ["test-models"]
   featured: false
   difficulty: "advanced"
+
+
+
+