diff --git a/Examples/biology/contactinhibitionhippoyap/contact-inhibition-hippo-yap.bngl b/Examples/biology/contactinhibitionhippoyap/contact-inhibition-hippo-yap.bngl index 11e200ad..47e81ca8 100644 --- a/Examples/biology/contactinhibitionhippoyap/contact-inhibition-hippo-yap.bngl +++ b/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 diff --git a/Examples/biology/contactinhibitionhippoyap/metadata.yaml b/Examples/biology/contactinhibitionhippoyap/metadata.yaml index 19056567..d3841b85 100644 --- a/Examples/biology/contactinhibitionhippoyap/metadata.yaml +++ b/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" + diff --git a/Examples/biology/ire1axbp1erstress/ire1a-xbp1-er-stress.bngl b/Examples/biology/ire1axbp1erstress/ire1a-xbp1-er-stress.bngl index f5d7d1cb..0bb75a6e 100644 --- a/Examples/biology/ire1axbp1erstress/ire1a-xbp1-er-stress.bngl +++ b/Examples/biology/ire1axbp1erstress/ire1a-xbp1-er-stress.bngl @@ -27,6 +27,7 @@ begin parameters XBP1_mRNA 1000 # The splicing substrate Target_mRNA 800 # RIDD substrate BiP_tot 300 + Unfolded_tot 10 end parameters begin molecule types @@ -34,21 +35,21 @@ begin molecule types 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 diff --git a/Examples/biology/ire1axbp1erstress/metadata.yaml b/Examples/biology/ire1axbp1erstress/metadata.yaml index 84193774..f3bf3762 100644 --- a/Examples/biology/ire1axbp1erstress/metadata.yaml +++ b/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" + + + +