// Created by libAntimony v2.8.0
model *Hoffmann2002_WT_IkBNFkB_Signaling()

  // Compartments and Species:
  compartment cytoplasm, nucleus;
  species IkBalpha in cytoplasm, NFkB in cytoplasm, IkBalpha_NFkB in cytoplasm;
  species IkBbeta in cytoplasm, IkBbeta_NFkB in cytoplasm, IkBeps in cytoplasm;
  species IkBeps_NFkB in cytoplasm, IKK_IkBalpha in cytoplasm, IKK_IkBalpha_NFkB in cytoplasm;
  species IKK in cytoplasm, IKK_IkBbeta in cytoplasm, IKK_IkBbeta_NFkB in cytoplasm;
  species IKK_IkBeps in cytoplasm, IKK_IkBeps_NFkB in cytoplasm, NFkB_nuc in nucleus;
  species IkBalpha_nuc in nucleus, IkBalpha_nuc_NFkB_nuc in nucleus, IkBbeta_nuc in nucleus;
  species IkBbeta_nuc_NFkB_nuc in nucleus, IkBeps_nuc in nucleus, IkBalpha_transcript in nucleus;
  species IkBbeta_transcript in nucleus, IkBeps_transcript in nucleus, IkBeps_nuc_NFkB_nuc in nucleus;

  // Assignment Rules:
  Total_IkBbeta := IkBbeta + IkBbeta_NFkB + IKK_IkBbeta + IKK_IkBbeta_NFkB;
  Total_IkBeps := IkBeps + IkBeps_NFkB + IKK_IkBeps + IKK_IkBeps_NFkB;
  Total_IkBalpha := IkBalpha + IkBalpha_NFkB + IKK_IkBalpha + IKK_IkBalpha_NFkB;
  Total_NFkBn := IkBbeta_nuc_NFkB_nuc + NFkB_nuc;

  // Rate Rules:
  fr_after_trigger' = trigger_value*(-0.5/(1 + (time - 2000))^2);

  // Reactions:
  v1: NFkB + IkBalpha -> IkBalpha_NFkB; cytoplasm*(a4*IkBalpha*NFkB - d4*IkBalpha_NFkB);
  v2: NFkB + IkBbeta -> IkBbeta_NFkB; cytoplasm*(a5*IkBbeta*NFkB - d5*IkBbeta_NFkB);
  v3: NFkB + IkBeps -> IkBeps_NFkB; cytoplasm*(a6*IkBeps*NFkB - d6*IkBeps_NFkB);
  v4: NFkB + IKK_IkBalpha -> IKK_IkBalpha_NFkB; cytoplasm*(a4*IKK_IkBalpha*NFkB - d4*IKK_IkBalpha_NFkB);
  v5: IKK_IkBalpha_NFkB => NFkB + IKK; cytoplasm*r4*IKK_IkBalpha_NFkB;
  v6: NFkB + IKK_IkBbeta -> IKK_IkBbeta_NFkB; cytoplasm*(a5*IKK_IkBbeta*NFkB - d5*IKK_IkBbeta_NFkB);
  v7: IKK_IkBbeta_NFkB => NFkB + IKK; cytoplasm*r5*IKK_IkBbeta_NFkB;
  v8: NFkB + IKK_IkBeps -> IKK_IkBeps_NFkB; cytoplasm*(a6*IKK_IkBeps*NFkB - d6*IKK_IkBeps_NFkB);
  v9: IKK_IkBeps_NFkB => NFkB + IKK; cytoplasm*r6*IKK_IkBeps_NFkB;
  v10: IkBalpha_NFkB => NFkB; cytoplasm*deg4*IkBalpha_NFkB;
  v11: IkBbeta_NFkB => NFkB; cytoplasm*deg4*IkBbeta_NFkB;
  v12: IkBeps_NFkB => NFkB; cytoplasm*deg4*IkBeps_NFkB;
  v13: NFkB -> NFkB_nuc; cytoplasm*k1*NFkB - nucleus*k01*NFkB_nuc;
  v14: NFkB_nuc + IkBalpha_nuc -> IkBalpha_nuc_NFkB_nuc; nucleus*(a4*IkBalpha_nuc*NFkB_nuc - d4*IkBalpha_nuc_NFkB_nuc);
  v15: NFkB_nuc + IkBbeta_nuc -> IkBbeta_nuc_NFkB_nuc; nucleus*(a5*IkBbeta_nuc*NFkB_nuc - d5*IkBbeta_nuc_NFkB_nuc);
  v16: NFkB_nuc + IkBeps_nuc -> IkBeps_nuc_NFkB_nuc; nucleus*(a6*IkBeps_nuc*NFkB_nuc - d6*IkBeps_nuc_NFkB_nuc);
  v17:  => IkBalpha_transcript; nucleus*tr2a;
  v18:  => IkBalpha_transcript; nucleus*tr2*NFkB_nuc^2;
  v19: IkBalpha_transcript => ; nucleus*tr3*IkBalpha_transcript;
  v20:  => IkBbeta_transcript; nucleus*tr2b;
  v21: IkBbeta_transcript => ; nucleus*tr3*IkBbeta_transcript;
  v22:  => IkBeps_transcript; nucleus*tr2e;
  v23: IkBeps_transcript => ; nucleus*tr3*IkBeps_transcript;
  v24: IKK + IkBalpha -> IKK_IkBalpha; cytoplasm*(a1*IkBalpha*IKK - d1*IKK_IkBalpha);
  v25:  => IkBalpha; nucleus*tr1*IkBalpha_transcript;
  v26: IkBalpha => ; cytoplasm*deg1*IkBalpha;
  v27: IkBalpha -> IkBalpha_nuc; cytoplasm*tp1*IkBalpha - nucleus*tp2*IkBalpha_nuc;
  v28: IKK + IkBbeta -> IKK_IkBbeta; cytoplasm*(a2*IkBbeta*IKK - d2*IKK_IkBbeta);
  v29:  => IkBbeta; nucleus*tr1*IkBbeta_transcript;
  v30: IkBbeta => ; cytoplasm*deg1*IkBbeta;
  v31: IkBbeta -> IkBbeta_nuc; cytoplasm*0.5*tp1*IkBbeta - nucleus*0.5*tp2*IkBbeta_nuc;
  v32: IKK + IkBeps -> IKK_IkBeps; cytoplasm*(a3*IkBeps*IKK - d3*IKK_IkBeps);
  v33:  => IkBeps; nucleus*tr1*IkBeps_transcript;
  v34: IkBeps => ; cytoplasm*deg1*IkBeps;
  v35: IkBeps -> IkBeps_nuc; cytoplasm*0.5*tp1*IkBeps - nucleus*0.5*tp2*IkBeps_nuc;
  v36: IKK + IkBalpha_NFkB -> IKK_IkBalpha_NFkB; cytoplasm*(a7*IKK*IkBalpha_NFkB - d1*IKK_IkBalpha_NFkB);
  v37: IkBalpha_nuc_NFkB_nuc => IkBalpha_NFkB; nucleus*k2*IkBalpha_nuc_NFkB_nuc;
  v38: IKK + IkBbeta_NFkB -> IKK_IkBbeta_NFkB; cytoplasm*(a8*IKK*IkBbeta_NFkB - d2*IKK_IkBbeta_NFkB);
  v39: IkBbeta_nuc_NFkB_nuc => IkBbeta_NFkB; nucleus*v39_k2_IkBbeta_nuc_NFkB_nuc*(fr_after_trigger + flag_for_after_trigger)*IkBbeta_nuc_NFkB_nuc;
  v40: IKK + IkBeps_NFkB -> IKK_IkBeps_NFkB; cytoplasm*(a9*IKK*IkBeps_NFkB - d3*IKK_IkBeps_NFkB);
  v41: IkBeps_nuc_NFkB_nuc => IkBeps_NFkB; nucleus*0.5*k2_eps*IkBeps_nuc_NFkB_nuc;
  v42: IKK_IkBalpha => IKK; cytoplasm*r1*IKK_IkBalpha;
  v43: IKK_IkBbeta => IKK; cytoplasm*r2*IKK_IkBbeta;
  v44: IKK_IkBeps => IKK; cytoplasm*r3*IKK_IkBeps;
  v45: IKK => ; cytoplasm*k02*IKK;

  // Events:
  event_0000001: at time >= 2000 && trigger_value == 0: flag_for_after_trigger = 0, trigger_value = 1, IKK = 0.1;

  // Species initializations:
  IkBalpha = 0.1;
  NFkB = 0.1;
  IkBalpha_NFkB = 0;
  IkBbeta = 0;
  IkBbeta_NFkB = 0;
  IkBeps = 0;
  IkBeps_NFkB = 0;
  IKK_IkBalpha = 0;
  IKK_IkBalpha_NFkB = 0;
  IKK = 0;
  IKK_IkBbeta = 0;
  IKK_IkBbeta_NFkB = 0;
  IKK_IkBeps = 0;
  IKK_IkBeps_NFkB = 0;
  NFkB_nuc = 0.001;
  IkBalpha_nuc = 0;
  IkBalpha_nuc_NFkB_nuc = 0;
  IkBbeta_nuc = 0;
  IkBbeta_nuc_NFkB_nuc = 0;
  IkBeps_nuc = 0;
  IkBalpha_transcript = 0;
  IkBbeta_transcript = 0;
  IkBeps_transcript = 0;
  IkBeps_nuc_NFkB_nuc = 0;

  // Compartment initializations:
  cytoplasm = 1;
  nucleus = 1;

  // Variable initializations:
  trigger_value = 0;
  flag_for_after_trigger = 0.5;
  a4 = 30;
  d4 = 0.03;
  a5 = 30;
  d5 = 0.03;
  a6 = 30;
  d6 = 0.03;
  r4 = 1.224;
  r5 = 0.45;
  r6 = 0.66;
  deg4 = 0.00135;
  k1 = 5.4;
  k01 = 0.0048;
  tr2a = 9.25e-005;
  tr2 = 0.99;
  tr3 = 0.0168;
  tr2b = 1.068e-005;
  tr2e = 7.62e-006;
  a1 = 1.35;
  d1 = 0.075;
  tr1 = 0.2448;
  deg1 = 0.00678;
  tp1 = 0.018;
  tp2 = 0.012;
  a2 = 0.36;
  d2 = 0.105;
  a3 = 0.54;
  d3 = 0.105;
  a7 = 11.1;
  k2 = 0.828;
  a8 = 2.88;
  k2_beta = 0.624;
  a9 = 4.2;
  k2_eps = 0.624;
  r1 = 0.2442;
  r2 = 0.09;
  r3 = 0.132;
  k02 = 0.0072;
  fr = 1;
  fr_after_trigger = 0.5;
  v39_k2_IkBbeta_nuc_NFkB_nuc = 0.0069;

  // Other declarations:
  var trigger_value, flag_for_after_trigger, fr, fr_after_trigger, Total_IkBbeta;
  var Total_IkBeps, Total_IkBalpha, Total_NFkBn;
  const cytoplasm, nucleus, a4, d4, a5, d5, a6, d6, r4, r5, r6, deg4, k1;
  const k01, tr2a, tr2, tr3, tr2b, tr2e, a1, d1, tr1, deg1, tp1, tp2, a2;
  const d2, a3, d3, a7, k2, a8, k2_beta, a9, k2_eps, r1, r2, r3, k02;

  // Unit definitions:
  unit substance = 1e-6 mole;
  unit time_unit = 60 second;

  // Display Names:
  substance is "micro mole";
  time_unit is "minutes";
  v1 is "NFkB-IkBalpha complex formation";
  v2 is "NFkB-IkBbeta complex formation";
  v3 is "NFkB-IkBeps complex formation";
  v4 is "NFkB-binary IKK IkBalpha complex formation";
  v5 is "IkBalpha degradation";
  v6 is "NFkB binary IKK IkBbeta complex formation";
  v7 is "IkBbeta degradation";
  v8 is "NFkB binary IKK IkBeps complex formation";
  v9 is "IkBeps degradation";
  v10 is "IkBalpha degradation";
  v11 is "IkBbeta degradation";
  v12 is "IkBeps degradation";
  v13 is "NFkB translocation";
  v14 is "NFkB-IkBalpha complex formation";
  v15 is "NFkB-IkBbeta complex formation";
  v16 is "NFkB-IkBeps complex formation";
  v17 is "IkBalpha transcription";
  v18 is "IkBalpha inducible transcription";
  v19 is "IkBalpha transcript degradation";
  v20 is "IkBbeta transcription";
  v21 is "IkBbeta transcript degradation";
  v22 is "IkBeps transcription";
  v23 is "IkBeps transcript degradation";
  v24 is "IKK-IkBalpha complex formation";
  v25 is "IkBalpha synthesis";
  v26 is "IkBalpha degradation";
  v27 is "IkBalpha translocation";
  v28 is "IKK-IkBbeta complex formation";
  v29 is "IkBbeta synthesis";
  v30 is "IkBbeta degradation";
  v31 is "IkBbeta translocation";
  v32 is "IKK-IkBeps complex formation";
  v33 is "IkBeps synthesis";
  v34 is "IkBeps degradation";
  v35 is "IkBeps translocation";
  v36 is "IKK-binary IkBalpha NFkB complex formation";
  v37 is "IkBalpha_NFkB translocation";
  v38 is "IKK binary IkBbeta NFkB complex formation";
  v39 is "IkBbeta_NFkB translocation";
  v40 is "IKK binary IkBeps NFkB complex formation";
  v41 is "IkBeps_NFkB translocation";
  v42 is "IkBalpha degradation";
  v43 is "IkBbeta degradation";
  v44 is "IkBeps degradation";
  v45 is "IKK consumption";
end