From 1ee4a4512f43c5a9965c7499441517ebd44f4a90 Mon Sep 17 00:00:00 2001 From: Michael Blinov Date: Mon, 6 Jul 2026 14:20:10 -0400 Subject: [PATCH 1/9] Fix seed species concentration Replaced number with parameter in seed species concentrations so MolClustPy works on it. --- .../contact-inhibition-hippo-yap.bngl | 3 ++- 1 file changed, 2 insertions(+), 1 deletion(-) 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 From 96a5ae89a9fe6926a401b4ffef3118a9298036c9 Mon Sep 17 00:00:00 2001 From: Michael Blinov Date: Mon, 6 Jul 2026 14:34:16 -0400 Subject: [PATCH 2/9] Changed metadata to include new keys, no old keys are changed except nfsim_compatible set to true --- .../contactinhibitionhippoyap/metadata.yaml | 41 +++++++++++++++++-- 1 file changed, 37 insertions(+), 4 deletions(-) diff --git a/Examples/biology/contactinhibitionhippoyap/metadata.yaml b/Examples/biology/contactinhibitionhippoyap/metadata.yaml index 19056567..edc48e48 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"] -category: "signaling" + +date: + last_tested: 2026-07-02 + +biol_categories: ["signaling"] + +comp_categories: ["other"] + compatibility: - bng2_compatible: true - simulation_methods: ["ode"] + rr_compatible: true + bnglviz_compatible: true + bng2_compatible: true + bngp_compatible: true # does not run with nf option + vcell_compatible: true # put actions outside of model + vcell_errors: + simulation_methods: ["ode", "ssa"] + nfsim_compatible: true # CHANGED! WARNING: Species with more than 20 molecules will be labeled with the Quasi method. + molclustpy_compatible: true # if set species concentration to variable instead of 1000 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" + \ No newline at end of file From 95983da6a5c0af4153294d9a555912187016896a Mon Sep 17 00:00:00 2001 From: Michael Blinov Date: Tue, 7 Jul 2026 14:49:12 -0400 Subject: [PATCH 3/9] Updated yaml; updated .bngl to be MolClustPy compatible --- .../ire1a-xbp1-er-stress.bngl | 13 +++--- .../biology/ire1axbp1erstress/metadata.yaml | 41 ++++++++++++++++++- 2 files changed, 46 insertions(+), 8 deletions(-) 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..bc6a74a6 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" + + + + From 904ddbeb4b509b8ce21f1fd544b4a3c1926cfbd4 Mon Sep 17 00:00:00 2001 From: Michael Blinov Date: Tue, 7 Jul 2026 15:17:42 -0400 Subject: [PATCH 4/9] Removed space after true --- Examples/biology/contactinhibitionhippoyap/metadata.yaml | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/Examples/biology/contactinhibitionhippoyap/metadata.yaml b/Examples/biology/contactinhibitionhippoyap/metadata.yaml index edc48e48..8b9463ed 100644 --- a/Examples/biology/contactinhibitionhippoyap/metadata.yaml +++ b/Examples/biology/contactinhibitionhippoyap/metadata.yaml @@ -23,7 +23,7 @@ compatibility: vcell_compatible: true # put actions outside of model vcell_errors: simulation_methods: ["ode", "ssa"] - nfsim_compatible: true # CHANGED! WARNING: Species with more than 20 molecules will be labeled with the Quasi method. + nfsim_compatible: true # CHANGED! WARNING: Species with more than 20 molecules will be labeled with the Quasi method. molclustpy_compatible: true # if set species concentration to variable instead of 1000 uses_compartments: false uses_energy: false @@ -54,4 +54,4 @@ playground: gallery_categories: ["test-models"] featured: false difficulty: "advanced" - \ No newline at end of file + From f5d6ada68c5c22473c89330ee4ceabe8518a630d Mon Sep 17 00:00:00 2001 From: Michael Blinov Date: Tue, 7 Jul 2026 15:18:55 -0400 Subject: [PATCH 5/9] Removed spaces after boolean --- Examples/biology/ire1axbp1erstress/metadata.yaml | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/Examples/biology/ire1axbp1erstress/metadata.yaml b/Examples/biology/ire1axbp1erstress/metadata.yaml index bc6a74a6..9e6f1e01 100644 --- a/Examples/biology/ire1axbp1erstress/metadata.yaml +++ b/Examples/biology/ire1axbp1erstress/metadata.yaml @@ -20,7 +20,7 @@ compatibility: rr_compatible: true bnglviz_compatible: true bng2_compatible: true - bngp_compatible: true + bngp_compatible: true vcell_compatible: false vcell_errors: "Encountered -> at line 69" simulation_methods: ["ode", "ssa"] @@ -28,7 +28,7 @@ compatibility: uses_energy: false uses_functions: true uses_compartments: false - nfsim_compatible: true + nfsim_compatible: true Features: uses_generate_network: true From ffea3e47af5268e7393d68d1f165962460ab9875 Mon Sep 17 00:00:00 2001 From: Michael Blinov Date: Tue, 7 Jul 2026 15:21:34 -0400 Subject: [PATCH 6/9] remove spaces after boolean --- .../biology/contactinhibitionhippoyap/metadata.yaml | 12 ++++++------ 1 file changed, 6 insertions(+), 6 deletions(-) diff --git a/Examples/biology/contactinhibitionhippoyap/metadata.yaml b/Examples/biology/contactinhibitionhippoyap/metadata.yaml index 8b9463ed..b528c338 100644 --- a/Examples/biology/contactinhibitionhippoyap/metadata.yaml +++ b/Examples/biology/contactinhibitionhippoyap/metadata.yaml @@ -18,13 +18,13 @@ comp_categories: ["other"] compatibility: rr_compatible: true bnglviz_compatible: true - bng2_compatible: true - bngp_compatible: true # does not run with nf option - vcell_compatible: true # put actions outside of model - vcell_errors: + bng2_compatible: true + bngp_compatible: true + vcell_compatible: true + vcell_errors: "to run put actions outside of model" simulation_methods: ["ode", "ssa"] - nfsim_compatible: true # CHANGED! WARNING: Species with more than 20 molecules will be labeled with the Quasi method. - molclustpy_compatible: true # if set species concentration to variable instead of 1000 + nfsim_compatible: true + molclustpy_compatible: true uses_compartments: false uses_energy: false uses_functions: true From f68865293af6abe0cab1b97277725f9bbdc168f8 Mon Sep 17 00:00:00 2001 From: Michael Blinov Date: Tue, 7 Jul 2026 15:24:44 -0400 Subject: [PATCH 7/9] Put small letter --- Examples/biology/contactinhibitionhippoyap/metadata.yaml | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/Examples/biology/contactinhibitionhippoyap/metadata.yaml b/Examples/biology/contactinhibitionhippoyap/metadata.yaml index b528c338..568e3b2a 100644 --- a/Examples/biology/contactinhibitionhippoyap/metadata.yaml +++ b/Examples/biology/contactinhibitionhippoyap/metadata.yaml @@ -30,7 +30,7 @@ compatibility: uses_functions: true -Features: +features: uses_generate_network: true default_sim_command: "ode" uses_energy: false From 7c35bb44f7ff45b0e55152ccb0ce2a37da0234a6 Mon Sep 17 00:00:00 2001 From: Michael Blinov Date: Tue, 7 Jul 2026 15:25:18 -0400 Subject: [PATCH 8/9] small letter for features --- Examples/biology/ire1axbp1erstress/metadata.yaml | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/Examples/biology/ire1axbp1erstress/metadata.yaml b/Examples/biology/ire1axbp1erstress/metadata.yaml index 9e6f1e01..f3bf3762 100644 --- a/Examples/biology/ire1axbp1erstress/metadata.yaml +++ b/Examples/biology/ire1axbp1erstress/metadata.yaml @@ -30,7 +30,7 @@ compatibility: uses_compartments: false nfsim_compatible: true -Features: +features: uses_generate_network: true default_sim_command: "ode" uses_totalrate: false From 7940dcfae0388d7f19e9a3e1a7f419de71638975 Mon Sep 17 00:00:00 2001 From: Michael Blinov Date: Tue, 7 Jul 2026 15:31:33 -0400 Subject: [PATCH 9/9] Add category field to metadata.yaml --- Examples/biology/contactinhibitionhippoyap/metadata.yaml | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/Examples/biology/contactinhibitionhippoyap/metadata.yaml b/Examples/biology/contactinhibitionhippoyap/metadata.yaml index 568e3b2a..d3841b85 100644 --- a/Examples/biology/contactinhibitionhippoyap/metadata.yaml +++ b/Examples/biology/contactinhibitionhippoyap/metadata.yaml @@ -11,8 +11,8 @@ tags: ["contact", "inhibition", "hippo", "yap", "mst", "lats", "tead"] date: last_tested: 2026-07-02 +category: "signaling" biol_categories: ["signaling"] - comp_categories: ["other"] compatibility: