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Add a corpus regression gate: parse_bngl vs a cached BNG2.pl golden
Asserts parse_bngl enumerates the same model entities BNG2.pl does, over 21 curated public community BNGL models (RuleHub, BNGL-Models) under tests/v1/bngl_corpus/. BNG2.pl's answers are cached in golden.json -- the entity name sets it emits from `writeModel` (its canonical parse, no network generation) -- so the test needs NO BNG2.pl and runs anywhere; it compares the reader against the frozen oracle. Seed species are compared by molecule composition to absorb BNG2.pl's pattern canonicalization (t vs t(), component reordering, @compartment prefix vs suffix). The models exercise every hardened reader path: line continuations, indexed and labeled declarations, block aliases, the $ clamp, compartmental BNGL, energy patterns, states/bonds, component reordering, bare-molecule seed species. The golden is regenerated deliberately (needs BNG2.pl) via `python tests/v1/test_bngl_corpus.py` and reviewed as a diff. Mirrors PyBNF's live-BNG2.pl gate (lanl/PyBNF); validated there over the full 895-model bng_parity corpus (894/894 BNG2.pl-accepted models agree). ruff clean; 21 passed without BNG2.pl. Refs: PEtab-dev/PEtab#436.
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‎tests/v1/bngl_corpus/An_2009.bngl‎

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begin parameters
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LPS_MD2_Bind 0.001
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LPS_MD2_Unbind 0.1
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LPS_CD14_Bind 0.001
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LPS_CD14_Unbind 0.1
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CD14_MD2_Bind 0.001
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CD14_MD2_Unbind 0.1
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LPS_TLR4_Bind 0.001
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LPS_TLR4_Unbind 0.1
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CD14_TLR4_Bind 0.001
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CD14_TLR4_Unbind 0.1
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MD2_TLR4_Bind 0.001
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MD2_TLR4_Unbind 0.1
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TLR4_Complex_Dimer_Bind 0.001
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TLR4_Complex_Dimer_Unbind 0.1
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RP1_TRIF_Bind 0.001
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RP1_TRIF_Unbind 0.1
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TRIF_TRAF6_Bind 0.001
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TRIF_TRAF6_Unbind 0.1
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RP1_TRAF6_Bind 0.001
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RP1_TRAF6_Unbind 0.1
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TLR4_TRAM_Bind 0.001
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TLR4_TRAM_Unbind 0.1
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TLR4TRAM_TRIF_Bind 0.001
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TLR4TRAM_TRIF_Unbind 0.1
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TRAF6_TRIF_Bind 0.001
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TRAF6_TRIF_Unbind 0.1
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TRAF6TRIF_TAK1_Activate 0.001
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MyD88_IRAK4_Bind 0.001
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MyD88_IRAK4_Unbind 0.1
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MyD88_IRAK1_Bind 0.001
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MyD88_IRAK1_Unbind 0.1
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IRAK1_IRAK4_Bind 0.001
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IRAK1_IRAK4_Unbind 0.1
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TLR4_MAL_Bind 0.001
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TLR4_MAL_Unbind 0.1
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TLR4MAL_MyD88_Bind 0.001
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TLR4MAL_MyD88_Unbind 0.1
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MyD88IRAK1_TRAF6_Bind 0.001
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MyD88IRAK1_TRAF6_B_Unbind 0.1
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MyD88IRAK1TRAF6_TAK1_Activate 0.001
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TRAF6_MyD88IRAK1_Bind 0.001
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TRAF6_MyD88IRAK1_Unbind 0.1
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TAK1_Ikk_Complex_Activate 0.001
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Ikk_complex_IkB_Phos 0.00001
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IkB_Proteasome23_Degrade 0.1
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p65_p50_Bind 0.001
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p65_p50_Unbind 0.1
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NFkB_DNA_A20_Bind 0.001
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A20_Transcription_Execute 1
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A20_TRAF6_Bind 0.001
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A20_TRAF6_Unbind 0.1
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NFkB_DNA_A20_Unbind 0.1
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NFkB_DNA_TNF_Bind 0.001
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NFkB_DNA_TNF_Unbind 0.1
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TNF_Transcription_Execute 1
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CD14_Init 10000
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MD2_Init 10000
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TLR_Init 10000
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LPS_Init 100
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TRAM_Init 10000
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MAL_Init 10000
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TRIF_Init 10000
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MyD88_Init 10000
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RP1_Init 10000
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IRAK1_Init 10000
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IRAK4_Init 10000
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TRAF6_Init 10000
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TAK1_Init 10000
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Ikk_Complex_Init 10000
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Proteasome23_Init 10000
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p65_Init 10000
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IkB_Init 10000
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p50_Init 10000
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DNA 2
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A20_Translation_Execute 0.1
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TNF_Translation_Execute 0.1
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TAK1_Degradation 0
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NFkB_Degredation 0
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A20_MyD88IRAK1TRAF6_Degrade 10
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A20_TRAF6TRIFRP1_Degrade 10
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A20_Init 0
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A20_Preconditioned 0
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Ikk_Degradation_Rate 0
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NFkB_DNA_IkB_Bind 0.001
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NFkB_DNA_IkB_Unbind 0.01
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IkB_Transcription_Execute 1
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IkB_Translation_Execute 0.1
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A20_IkkAct_Deactivate 10
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IkB_DegradeNFkB 0.001
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NFkB_Inactive_Cytoplasm 10000
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NFkB_IkB_Bind 0.001
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NFkB_Translocation_Nucleus 0.01
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NFkB_IkB_Unbind 0.0001
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TAK1_Deactivation 0.10
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Ikk_Deactivation 0
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TNF_Degrade 0.0005
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A20_Degrade 0.0001
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end parameters
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begin molecule types
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CD14(TLR4,MD2,LPS)
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MD2(CD14,TLR4,LPS)
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TLR4(MAL,TRAM,TLR4,CD14,MD2,LPS)
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TRAM(TLR4,TRIF)
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TRIF(TRAM,TRAF6,RIP1,TRAF4,SARM)
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SARM(TRIF)
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TRAF4(TRAF6,TAK1,TRIF)
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IRAK1(IRAK4,MyD88,Tollip,TRAF6)
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Tollip(IRAK1)
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IRAK4(Myd88,IRAKM,IRAK1)
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IRAKM(IRAK4)
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RP1(TRIF,TRAF6,TAK1,p38)
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TRAF6(IRAK1,TRIF,RP1,TAK1,TRAF4,A20,JNK,p38)
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A20(TRAF6)
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MyD88(MAL,IRAK1,IRAK4,MyD88s)
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MyD88s(MyD88,IRAK1)
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MAL(TLR4,MyD88,SOCS1)
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LPS(MD2,TLR4,CD14,LPS)
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TAK1(TRAF6,Activation~No~Yes)
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Ikk_Complex(Activation~No~Yes)
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IkB(Phos~No~Yes,p65,p50,Degrade~No~Yes)
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Proteasome26s(IkB)
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TNF(TNFr)
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TNFmRNA(Translation~On~Off)
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A20mRNA(Translation~On~Off)
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iNOSmRNA(Translation~On~Off)
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IkBmRNA(Translation~On~Off)
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DNA(A20,TNF,iNOS,IL10,IkB,c,c)
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Trash(c)
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Administer(c)
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NFkB(Transcription~No~Yes,Activation~No~Yes,Location~Cytoplasm~Nucleus)
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end molecule types
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begin seed species
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CD14: CD14(TLR4,MD2,LPS) CD14_Init
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MD2: MD2(CD14,TLR4,LPS) MD2_Init
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TLR4: TLR4(MAL,TRAM,TLR4,CD14,MD2,LPS) TLR_Init
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TRAM: TRAM(TLR4,TRIF) TRAM_Init
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MAL: MAL(TLR4,MyD88,SOCS1) MAL_Init
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TRIF: TRIF(TRAM,TRAF6,RIP1,SARM,TRAF4) TRIF_Init
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MyD88: MyD88(MAL,IRAK1,IRAK4,MyD88s) MyD88_Init
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RP1: RP1(TRIF,TRAF6,TAK1,p38) RP1_Init
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IRAK1: IRAK1(IRAK4,MyD88,Tollip,TRAF6) IRAK1_Init
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IRAK4: IRAK4(Myd88,IRAKM,IRAK1) IRAK4_Init
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TRAF6: TRAF6(IRAK1,TRIF,RP1,TAK1,TRAF4,A20,JNK,p38) TRAF6_Init
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TAK1: TAK1(TRAF6,Activation~No) TAK1_Init
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Ikk_Complex: Ikk_Complex(Activation~No) Ikk_Complex_Init
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Proteasome23: Proteasome26s(IkB) Proteasome23_Init
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IkB: IkB(Phos~No,p65,p50,Degrade~No) IkB_Init
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DNA: DNA(A20,TNF,iNOS,IL10,IkB,c,c) DNA
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LPS: LPS(MD2,TLR4,CD14,LPS) LPS_Init
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A20: A20(TRAF6) A20_Preconditioned
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NFkB_Inactive_Cytoplasm: NFkB(Transcription~No,Activation~No,Location~Cytoplasm) NFkB_Inactive_Cytoplasm
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end seed species
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begin reaction rules
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LPS_MD2: LPS(MD2,TLR4,CD14,LPS)+MD2(CD14,TLR4,LPS)<->LPS(MD2!0,TLR4,CD14,LPS).MD2(CD14,TLR4,LPS!0) LPS_MD2_Bind,LPS_MD2_Unbind
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LPS_MD2_CD14: LPS(MD2!0,TLR4,CD14,LPS).MD2(CD14,TLR4,LPS!0)+CD14(TLR4,MD2,LPS)<->LPS(MD2!0,TLR4,CD14!1,LPS).MD2(CD14,TLR4,LPS!0).CD14(TLR4,MD2,LPS!1) LPS_CD14_Bind,LPS_CD14_Unbind
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LPS_MD2_CD14_TLR4: LPS(MD2!0,TLR4,CD14!1,LPS).MD2(CD14,TLR4,LPS!0).CD14(TLR4,MD2,LPS!1) + TLR4(MAL,TRAM,TLR4,CD14,MD2,LPS) <-> LPS(MD2!0,TLR4!2,CD14!1,LPS).MD2(CD14!3,TLR4!4,LPS!0).CD14(TLR4!5,MD2!3,LPS!1).TLR4(MAL,TRAM,TLR4,CD14!5,MD2!4,LPS!2) LPS_TLR4_Bind,LPS_TLR4_Unbind
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TLR4_Dimerization: TLR4(TLR4,CD14!+,LPS!+,MD2!+)+TLR4(TLR4,CD14!+,MD2!+,LPS!+)<->TLR4(TLR4!0,CD14!+,LPS!+,MD2!+).TLR4(TLR4!0,CD14!+,LPS!+,MD2!+) TLR4_Complex_Dimer_Bind,TLR4_Complex_Dimer_Unbind
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TLR4_TRAM: TLR4(TLR4!+,CD14!+,LPS!+,MD2!+,TRAM,MAL)+TRAM(TLR4,TRIF)<->TRAM(TLR4!0,TRIF).TLR4(TLR4!+,CD14!+,LPS!+,MD2!+,TRAM!0,MAL) TLR4_TRAM_Bind,TLR4_TRAM_Unbind
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TLR4TRAM_TRIF: TRAM(TLR4!0,TRIF).TLR4(TLR4!+,CD14!+,LPS!+,MD2!+,TRAM!0,MAL)+TRIF(TRAM,TRAF6!+,RIP1!+,TRAF4,SARM)<->TRAM(TLR4!0,TRIF!1).TLR4(TLR4!+,CD14!+,LPS!+,MD2!+,TRAM!0,MAL).TRIF(TRAM!1,TRAF6!+,RIP1!+,TRAF4,SARM) TLR4TRAM_TRIF_Bind,TLR4TRAM_TRIF_Unbind
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TLR4TRAMTRIFTRAF6_TAK1: TRAM(TLR4!0,TRIF!1).TLR4(TLR4!+,CD14!+,LPS!+,MD2!+,TRAM!0,MAL).TRIF(TRAM!1,TRAF6!+,RIP1!+,TRAF4,SARM)+TAK1(TRAF6,Activation~No)->TRAM(TLR4!0,TRIF!1).TLR4(TLR4!+,CD14!+,LPS!+,MD2!+,TRAM!0,MAL).TRIF(TRAM!1,TRAF6!+,RIP1!+,TRAF4,SARM)+TAK1(TRAF6,Activation~Yes) TRAF6TRIF_TAK1_Activate
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MyD88_IRAK4: MyD88(MAL,IRAK1,IRAK4,MyD88s)+IRAK4(Myd88,IRAKM,IRAK1)<->MyD88(MAL,IRAK1,IRAK4!0,MyD88s).IRAK4(Myd88!0,IRAKM,IRAK1) MyD88_IRAK4_Bind,MyD88_IRAK4_Unbind
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MyD88_IRAK1: MyD88(MAL,IRAK1,IRAK4!0,MyD88s).IRAK4(Myd88!0,IRAKM,IRAK1)+IRAK1(IRAK4,MyD88,Tollip,TRAF6)<->IRAK1(IRAK4,MyD88!0,Tollip,TRAF6).MyD88(MAL,IRAK1!0,IRAK4!1,MyD88s).IRAK4(Myd88!1,IRAKM,IRAK1) MyD88_IRAK1_Bind,MyD88_IRAK1_Unbind
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TNF_Translation: TNFmRNA(Translation~On)->TNFmRNA(Translation~Off)+TNF(TNFr) TNF_Translation_Execute
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A20_Translation: A20mRNA(Translation~On)->A20mRNA(Translation~Off)+A20(TRAF6) A20_Translation_Execute
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TAK1_Degrade: TAK1(TRAF6,Activation~Yes)->Trash(c) TAK1_Degradation
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TLR4_MAL: TLR4(TLR4!+,CD14!+,LPS!+,MD2!+,TRAM,MAL)+MAL(TLR4,MyD88,SOCS1)<->TLR4(TLR4!+,CD14!+,LPS!+,MD2!+,TRAM,MAL!0).MAL(SOCS1,TLR4!0,MyD88) TLR4_MAL_Bind,TLR4_MAL_Unbind
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TLR4MAL_MyD88: TLR4(TLR4!+,CD14!+,LPS!+,MD2!+,TRAM,MAL!0).MAL(TLR4!0,MyD88,SOCS1) + IRAK1(IRAK4,MyD88!2,Tollip,TRAF6).MyD88(MAL,IRAK1!2,IRAK4!1,MyD88s).IRAK4(Myd88!1,IRAKM,IRAK1) <-> TLR4(TLR4!+,CD14!+,LPS!+,MD2!+,TRAM,MAL!0).MAL(TLR4!0,MyD88!4,SOCS1).IRAK1(IRAK4,MyD88!2,Tollip,TRAF6).MyD88(MAL!4,IRAK1!2,IRAK4!3,MyD88s).IRAK4(Myd88!3,IRAKM,IRAK1) TLR4MAL_MyD88_Bind,TLR4MAL_MyD88_Unbind
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MyD88IRAK1_TRAF6: TRAF6(IRAK1,TRIF,RP1,TRAF4,A20,JNK,p38,TAK1)+TLR4(TLR4!+,CD14!+,LPS!+,MD2!+,TRAM,MAL!0).MAL(TLR4!0,MyD88!1,SOCS1).IRAK1(IRAK4,MyD88!2,Tollip,TRAF6).MyD88(MAL!1,IRAK1!2,IRAK4!3,MyD88s).IRAK4(Myd88!3,IRAKM,IRAK1)<->TRAF6(IRAK1!4,TRIF,RP1,TRAF4,A20,JNK,p38,TAK1).TLR4(TLR4!+,CD14!+,LPS!+,MD2!+,TRAM,MAL!0).MAL(TLR4!0,MyD88!1,SOCS1).IRAK1(IRAK4,MyD88!2,Tollip,TRAF6!4).MyD88(MAL!1,IRAK1!2,IRAK4!3,MyD88s).IRAK4(Myd88!3,IRAKM,IRAK1) MyD88IRAK1_TRAF6_Bind,MyD88IRAK1_TRAF6_B_Unbind
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A20_MyD88IRAK1TRAF6: TRAF6(IRAK1!0,TRIF,RP1,TRAF4,A20,JNK,p38,TAK1).TLR4(TLR4!+,CD14!+,LPS!+,MD2!+,TRAM,MAL!1).MAL(TLR4!1,MyD88!2,SOCS1).IRAK1(IRAK4,MyD88!3,Tollip,TRAF6!0).MyD88(MAL!2,IRAK1!3,IRAK4!4,MyD88s).IRAK4(Myd88!4,IRAKM,IRAK1)+A20(TRAF6)->TRAF6(IRAK1,TRIF,RP1,TAK1,TRAF4,A20,JNK,p38)+TLR4(TLR4!+,CD14!+,LPS!+,MD2!+,TRAM,MAL!1).MAL(TLR4!1,MyD88!2,SOCS1).IRAK1(IRAK4,MyD88!3,Tollip,TRAF6).MyD88(MAL!2,IRAK1!3,IRAK4!4,MyD88s).IRAK4(Myd88!4,IRAKM,IRAK1)+A20(TRAF6) A20_MyD88IRAK1TRAF6_Degrade
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MyD88IRAK1TRAF6_TAK1: TRAF6(IRAK1!0,TRIF,RP1,TRAF4,A20,JNK,p38,TAK1).TLR4(TLR4!+,CD14!+,LPS!+,MD2!+,TRAM,MAL!1).MAL(TLR4!1,MyD88!2,SOCS1).IRAK1(IRAK4,MyD88!3,Tollip,TRAF6!0).MyD88(MAL!2,IRAK1!3,IRAK4!4,MyD88s).IRAK4(Myd88!4,IRAKM,IRAK1)+TAK1(TRAF6,Activation~No)->TRAF6(IRAK1!0,TRIF,RP1,TRAF4,A20,JNK,p38,TAK1).TLR4(TLR4!+,CD14!+,LPS!+,MD2!+,TRAM,MAL!1).MAL(TLR4!1,MyD88!2,SOCS1).IRAK1(IRAK4,MyD88!3,Tollip,TRAF6!0).MyD88(MAL!2,IRAK1!3,IRAK4!4,MyD88s).IRAK4(Myd88!4,IRAKM,IRAK1)+TAK1(TRAF6,Activation~Yes) MyD88IRAK1TRAF6_TAK1_Activate
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IkB_Translation: IkBmRNA(Translation~On)->IkBmRNA(Translation~Off)+IkB(Phos~No,p65,p50,Degrade~No) IkB_Translation_Execute
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TRIF_RP1: TRIF(TRAM,TRAF6,RIP1,TRAF4,SARM)+RP1(TRIF,TRAF6,TAK1,p38)<->RP1(TRIF!0,TRAF6,TAK1,p38).TRIF(TRAM,TRAF6,RIP1!0,TRAF4,SARM) RP1_TRIF_Bind,RP1_TRIF_Unbind
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TRIF_TRAF6: RP1(TRIF!0,TRAF6,TAK1,p38).TRIF(TRAM,TRAF6,RIP1!0,TRAF4,SARM)+TRAF6(IRAK1,TRIF,RP1,TAK1,TRAF4,A20,JNK,p38)<->RP1(TRIF!0,TRAF6!1,TAK1,p38).TRIF(TRAM,TRAF6!2,RIP1!0,TRAF4,SARM).TRAF6(IRAK1,TRIF!2,RP1!1,TAK1,TRAF4,A20,JNK,p38) TRIF_TRAF6_Bind,TRIF_TRAF6_Unbind
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A20_IkkAct_Deactivate: A20(TRAF6)+Ikk_Complex(Activation~Yes)->A20(TRAF6)+Ikk_Complex(Activation~No) A20_IkkAct_Deactivate
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A20_TRAF6TRIFRP1_Degrade: A20(TRAF6)+RP1(TRIF!0,TRAF6!1,TAK1,p38).TRIF(TRAM,TRAF6!2,RIP1!0,TRAF4,SARM).TRAF6(IRAK1,TRIF!2,RP1!1,TAK1,TRAF4,A20,JNK,p38)->TRAF6(IRAK1,TRIF,RP1,TAK1,TRAF4,A20,JNK,p38)+RP1(TRIF,TRAF6,TAK1,p38)+TRIF(TRAM,TRAF6,RIP1,TRAF4,SARM)+A20(TRAF6) A20_TRAF6TRIFRP1_Degrade
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Ikk_complex_IkB_Phos: Ikk_Complex(Activation~Yes)+NFkB(Transcription~No,Activation~No!0!1,Location~Cytoplasm).IkB(Phos~No,p65!0,p50!1,Degrade~No)->Ikk_Complex(Activation~Yes)+NFkB(Transcription~No,Activation~No!0!1,Location~Cytoplasm).IkB(p65!0,p50!1,Degrade~No,Phos~Yes) Ikk_complex_IkB_Phos
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NFkB_Translocation_Nucleus: NFkB(Transcription~No,Activation~Yes,Location~Cytoplasm)<->NFkB(Transcription~No,Activation~Yes,Location~Nucleus) NFkB_Translocation_Nucleus,NFkB_Translocation_Nucleus
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NFkB_DNA_A20: NFkB(Transcription~No,Activation~Yes,Location~Nucleus)+DNA(A20)<->DNA(A20!0).NFkB(Transcription~Yes!0,Activation~Yes,Location~Nucleus) NFkB_DNA_A20_Bind,NFkB_DNA_A20_Unbind
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IkB_DegradeNFkBA20: DNA(A20!0).NFkB(Transcription~Yes!0,Activation~Yes,Location~Nucleus)+IkB(Phos~No,p65,p50,Degrade~No)->DNA(A20)+NFkB(Transcription~No,Activation~No!0!1,Location~Cytoplasm).IkB(Phos~No,p65!0,p50!1,Degrade~No) IkB_DegradeNFkB
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NFkB_DNA_TNF: NFkB(Transcription~No,Activation~Yes,Location~Nucleus)+DNA(TNF)<->DNA(TNF!0).NFkB(Transcription~Yes!0,Activation~Yes,Location~Nucleus) NFkB_DNA_TNF_Bind,NFkB_DNA_TNF_Unbind
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NFkB_DNA_IkB: NFkB(Transcription~No,Activation~Yes,Location~Nucleus)+DNA(IkB)<->DNA(IkB!0).NFkB(Transcription~Yes!0,Activation~Yes,Location~Nucleus) NFkB_DNA_IkB_Bind,NFkB_DNA_IkB_Unbind
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IkB_Proteasome23_Degrade: Proteasome26s(IkB)+NFkB(Transcription~No,Activation~No!0!1,Location~Cytoplasm).IkB(Phos~Yes,p65!0,p50!1,Degrade~No)->IkB(Phos~Yes,p65,p50,Degrade~Yes!0).Proteasome26s(IkB!0)+NFkB(Transcription~No,Activation~Yes,Location~Cytoplasm) IkB_Proteasome23_Degrade
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#NFkB_IkB_Bind: NFkB(Location~Cytoplasm,Activation~*)+IkB(Phos~No,p65,p50,Degrade~No)<->NFkB(Activation~*!0!1,Location~Cytoplasm).IkB(Phos~No,p65!0,p50!1,Degrade~No) NFkB_IkB_Bind,NFkB_IkB_Unbind
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NFkB_IkB_Bind: NFkB(Location~Cytoplasm,Activation)+IkB(Phos~No,p65,p50,Degrade~No)<->NFkB(Activation!0!1,Location~Cytoplasm).IkB(Phos~No,p65!0,p50!1,Degrade~No) NFkB_IkB_Bind,NFkB_IkB_Unbind
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Proteasome23_Release: IkB(Degrade~Yes!0).Proteasome26s(IkB!0)->IkB(Degrade~Yes)+Proteasome26s(IkB) IkB_Proteasome23_Degrade
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IkB_Transcription_Execute: DNA(IkB!0).NFkB(Transcription~Yes!0,Activation~Yes,Location~Nucleus)->IkBmRNA(Translation~On)+DNA(IkB!0).NFkB(Transcription~Yes!0,Activation~Yes,Location~Nucleus) IkB_Transcription_Execute
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A20_Transcription_Execute: DNA(A20!0).NFkB(Transcription~Yes!0,Activation~Yes,Location~Nucleus)->A20mRNA(Translation~On)+DNA(A20!0).NFkB(Transcription~Yes!0,Activation~Yes,Location~Nucleus) A20_Transcription_Execute
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TNF_Transcription_Execute: DNA(TNF!0).NFkB(Transcription~Yes!0,Activation~Yes,Location~Nucleus)->TNFmRNA(Translation~On)+DNA(TNF!0).NFkB(Transcription~Yes!0,Activation~Yes,Location~Nucleus) TNF_Transcription_Execute
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TAK1_Deactivation: TAK1(TRAF6,Activation~Yes)->TAK1(TRAF6,Activation~No) TAK1_Deactivation
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Ikk_Deactivation: Ikk_Complex(Activation~Yes)->Ikk_Complex(Activation~No) Ikk_Deactivation
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TAK1_Ikk_Complex_Activate: TAK1(TRAF6,Activation~Yes)+Ikk_Complex(Activation~No)->TAK1(TRAF6,Activation~Yes)+Ikk_Complex(Activation~Yes) TAK1_Ikk_Complex_Activate
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TNF_Degrade: TNF(TNFr)->Trash(c) TNF_Degrade
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A20_Degrade: A20(TRAF6)->Trash(c) A20_Degrade
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IkB_DegradeNFkBDNAIkB: DNA(IkB!0).NFkB(Transcription~Yes!0,Activation~Yes,Location~Nucleus)+IkB(Phos~No,p65,p50,Degrade~No)->DNA(IkB)+IkB(Phos~No,p65!0,p50!1,Degrade~No).NFkB(Transcription~No,Activation~No!0!1,Location~Cytoplasm) IkB_DegradeNFkB
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IkB_DegradeNFkBDNA_TNF: DNA(TNF!0).NFkB(Transcription~Yes!0,Activation~Yes,Location~Nucleus)+IkB(Phos~No,p65,p50,Degrade~No)->DNA(TNF)+IkB(Phos~No,p65!0,p50!1,Degrade~No).NFkB(Transcription~No,Activation~No!0!1,Location~Cytoplasm) IkB_DegradeNFkB
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end reaction rules
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begin observables
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Molecules TNF TNF(TNFr)
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Molecules Activated_TAK1 TAK1(TRAF6,Activation~Yes)
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Molecules Activated_Ikk_complex Ikk_Complex(Activation~Yes)
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Molecules A20 A20(TRAF6)
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Molecules NFkB_Active_Cyto NFkB(Transcription~No,Activation~Yes,Location~Cytoplasm)
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Molecules NFkB_Active_Nucleus NFkB(Transcription~No,Activation~Yes,Location~Nucleus)
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Molecules IkB_Degraded IkB(Degrade~Yes)
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Molecules IkB_active IkB(Degrade~No)
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#Molecules NFkB_Inactive NFkB(Activation~*!+)
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Molecules NFkB_Inactive NFkB(Activation!+)
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Molecules NonBoundNonPhos_IkB IkB(Phos~No,p65,p50,Degrade~No)
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Molecules IkBmRNA_Off IkBmRNA(Translation~Off)
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Molecules NFkB_DNA_IkB DNA(IkB!0).NFkB(Transcription~Yes!0,Activation~Yes,Location~Nucleus)
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Molecules Phos_IkB_NFkB NFkB(Transcription~No,Activation~No!0!1,Location~Cytoplasm).IkB(Phos~Yes,p65!0,p50!1,Degrade~No)
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Molecules IkB_Prot26s IkB(Phos~Yes,p65,p50,Degrade~Yes!0).Proteasome26s(IkB!0)
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#Molecules Unbound_Cyto_NFkB NFkB(Location~Cytoplasm,Activation)
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Molecules Unbound_Cyto_NFkB NFkB(Location~Cytoplasm,Activation)
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#Molecules Inactive_Cyto_NFkB NFkB(Activation~*!0!1,Location~Cytoplasm).IkB(Phos~No,p65!0,p50!1,Degrade~No)
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Molecules Inactive_Cyto_NFkB NFkB(Activation!0!1,Location~Cytoplasm).IkB(Phos~No,p65!0,p50!1,Degrade~No)
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Molecules TNFmRNA_Off TNFmRNA(Translation~Off)
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Molecules TNF_NFkB_DNA DNA(TNF!0).NFkB(Transcription~Yes!0,Activation~Yes,Location~Nucleus)
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Molecules A20_NFkB_DNA DNA(A20!0).NFkB(Transcription~Yes!0,Activation~Yes,Location~Nucleus)
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end observables
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generate_network({overwrite=>1});
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setConcentration("LPS(MD2,TLR4,CD14,LPS)",0);
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simulate_ode({suffix=>"equil",t_end=>50000,n_steps=>10,atol=>1e-12,rtol=>1e-12,sparse=>1,steady_state=>1});
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#BEGIN SIMULATION
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setConcentration("LPS(MD2,TLR4,CD14,LPS)","LPS_Init");
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writeSBML();
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writeMfile();
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simulate_ode({t_end=>100000,n_steps=>500,atol=>1e-12,rtol=>1e-12,sparse=>0});

‎tests/v1/bngl_corpus/Barua_2009__PATCHED.bngl‎

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begin parameters
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kon_dimer 1.0 # units = 1/(uM.s)
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koff_dimer 0.1 # units = 1/s
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kon_SH2 1.0 # units = 1/(uM.s)
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koff_SH2 0.1 # units = 1/s
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kphos_slow 0.1 # units = 1/s
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kphos_fast 1.0 # units = 1/s
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Jtot 0.000014 # units = uM
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Stot 0.1 # units = uM
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end parameters
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begin molecule types
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S(SH2,DD)
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J(Y1~P,Y~U~P)
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end molecule types
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begin species
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S(SH2,DD) Stot
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J(Y1~P,Y~U) Jtot
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end species
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begin reaction rules
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# JAK2-SH2B interaction
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J(Y1~P) + S(SH2) <-> J(Y1~P!1).S(SH2!1) kon_SH2, koff_SH2
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# SH2B dimerization
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S(DD) + S(DD) <-> S(DD!1).S(DD!1) kon_dimer, koff_dimer
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# JAK2 phosphorylation
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J(Y~U,Y1!1).S(SH2!1,DD!2).S(DD!2,SH2!3).J(Y1!3,Y~U) -> J(Y~P,Y1!1).S(SH2!1,DD!2).S(DD!2,SH2!3).J(Y1!3,Y~U) kphos_slow
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J(Y~U,Y1!1).S(SH2!1,DD!2).S(DD!2,SH2!3).J(Y1!3,Y~P) -> J(Y~P,Y1!1).S(SH2!1,DD!2).S(DD!2,SH2!3).J(Y1!3,Y~P) kphos_fast
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end reaction rules
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begin observables
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Molecules J_mono J(Y1~P)
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Molecules JS J(Y1~P!1).S(SH2!1,DD)
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Molecules JSS J(Y1~P!1).S(SH2!1,DD!2).S(SH2,DD!2)
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Molecules JSSJ J.J
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Molecules J_active J(Y~P)
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Molecules J_inactive J(Y~U)
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end observables
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generate_network({overwrite=>1, max_stoich=>{J=>2}});
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simulate_ode({t_end=>10000, n_steps=>10000,atol=>1e-08,rtol=>1e-08,sparse=>1});

‎tests/v1/bngl_corpus/Chattaraj_2021.bngl‎

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# Clustering of three signaling molecules - Nephrin, Nck and NWASP
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# References:
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# 1. A. Chattaraj, M. L. Blinov and L. M. Loew. "The solubility product extends the buffering concept
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# to heterotypic biomolecular condensates." eLife 2021, Vol. 10 Pages e67176, DOI: 10.7554/eLife.67176 (Figure 6)
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# 2. A. Chattaraj and L. M. Loew. "The maximum solubility product marks the threshold for condensation
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# of multivalent biomolecules". bioRxiv 2022, DOI: 10.1101/2022.10.04.510809 (Figure 6B)
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begin model
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begin parameters
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# 1: Nephrin, 2: Nck, 3: NWASP
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# Kd: binding affinity, kon: binding rate constant, koff: unbinding rate constant
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kd_12 3500
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kd_23 3500
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koff_23 1000
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kon_23 koff_23/kd_23
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koff_12 1000
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kon_12 koff_12/kd_12
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end parameters
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begin molecule types
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Nephrin(pY1,pY2,pY3)
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Nck(S1,S2,S3,Sh2)
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NWASP(p1,p2,p3,p4,p5,p6)
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end molecule types
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begin seed species
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1 Nephrin(pY1,pY2,pY3) 300
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2 Nck(S1,S2,S3,Sh2) 900
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3 NWASP(p1,p2,p3,p4,p5,p6) 450
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end seed species
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begin observables
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Molecules tot_Nck Nck()
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Molecules free_Nck Nck(S1,S2,S3,Sh2)
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Molecules tot_NWASP NWASP()
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Molecules free_NWASP NWASP(p1,p2,p3,p4,p5,p6)
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Molecules tot_Nephrin Nephrin()
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Molecules free_Nephrin Nephrin(pY1,pY2,pY3)
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Molecules fully_bound_Nephrin Nephrin(pY1!+,pY2!+,pY3!+)
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Molecules fully_bound_Nck Nck(S1!+,S2!+,S3!+,Sh2!+)
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Molecules fully_bound_NWASP NWASP(p1!+,p2!+,p3!+,p4!+,p5!+,p6!+)
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Molecules cluster_neph_nck_nw Nephrin().Nck().NWASP()
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Molecules cluster_nck_nw Nck().NWASP()
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end observables
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begin reaction rules
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_01_S1_P1: Nck(S1) + NWASP(p1) <-> Nck(S1!1).NWASP(p1!1) kon_23, koff_23
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_02_S2_P1: Nck(S2) + NWASP(p1) <-> Nck(S2!1).NWASP(p1!1) kon_23, koff_23
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_03_S3_P1: Nck(S3) + NWASP(p1) <-> Nck(S3!1).NWASP(p1!1) kon_23, koff_23
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_06_S3_P2: Nck(S3) + NWASP(p2) <-> Nck(S3!1).NWASP(p2!1) kon_23, koff_23
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_05_S2_P2: Nck(S2) + NWASP(p2) <-> Nck(S2!1).NWASP(p2!1) kon_23, koff_23
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_04_S1_P2: Nck(S1) + NWASP(p2) <-> Nck(S1!1).NWASP(p2!1) kon_23, koff_23
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_08_S2_P3: Nck(S2) + NWASP(p3) <-> Nck(S2!1).NWASP(p3!1) kon_23, koff_23
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_07_S1_P3: Nck(S1) + NWASP(p3) <-> Nck(S1!1).NWASP(p3!1) kon_23, koff_23
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_09_S3_P3: Nck(S3) + NWASP(p3) <-> Nck(S3!1).NWASP(p3!1) kon_23, koff_23
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_10_S1_P4: Nck(S1) + NWASP(p4) <-> Nck(S1!1).NWASP(p4!1) kon_23, koff_23
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_11_S2_P4: Nck(S2) + NWASP(p4) <-> Nck(S2!1).NWASP(p4!1) kon_23, koff_23
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_12_S3_P4: Nck(S3) + NWASP(p4) <-> Nck(S3!1).NWASP(p4!1) kon_23, koff_23
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_13_S1_P5: Nck(S1) + NWASP(p5) <-> Nck(S1!1).NWASP(p5!1) kon_23, koff_23
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_14_S2_P5: Nck(S2) + NWASP(p5) <-> Nck(S2!1).NWASP(p5!1) kon_23, koff_23
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_15_S3_P5: Nck(S3) + NWASP(p5) <-> Nck(S3!1).NWASP(p5!1) kon_23, koff_23
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_16_S1_P6: Nck(S1) + NWASP(p6) <-> Nck(S1!1).NWASP(p6!1) kon_23, koff_23
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_17_S3_P6: Nck(S3) + NWASP(p6) <-> Nck(S3!1).NWASP(p6!1) kon_23, koff_23
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_18_S2_P6: Nck(S2) + NWASP(p6) <-> Nck(S2!1).NWASP(p6!1) kon_23, koff_23
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_19_pY1_sh2: Nephrin(pY1) + Nck(Sh2) <-> Nephrin(pY1!1).Nck(Sh2!1) kon_12, koff_12
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_20_pY2_sh2: Nephrin(pY2) + Nck(Sh2) <-> Nephrin(pY2!1).Nck(Sh2!1) kon_12, koff_12
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_21_pY3_sh2: Nephrin(pY3) + Nck(Sh2) <-> Nephrin(pY3!1).Nck(Sh2!1) kon_12, koff_12
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end reaction rules
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end model
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writeXML()

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