// Created by libAntimony v2.8.0
model *Model_1()

  // Compartments and Species:
  compartment Cell;
  species $NGF in Cell, TrkA in Cell, $pro_TrkA in Cell, pTrkA in Cell, pTrkA_Akt in Cell;
  species Akt in Cell, pAkt in Cell, S6 in Cell, pAkt_S6 in Cell, pS6 in Cell;
  species NGF_TrkA in Cell;

  // Assignment Rules:
  NGF := NGF_conc_step + piecewise(NGF_conc_pulse, time <= pulse_time, 0) + (NGF_conc_ramp*time)/ramp_time;
  pTrkA_total := (pTrkA + pTrkA_Akt)*pTrkA_scaleFactor;
  pAkt_total := (pAkt + pAkt_S6)*pAkt_scaleFactor;
  pS6_total := pS6*pS6_scaleFactor;

  // Reactions:
  reaction_1: $NGF + TrkA -> NGF_TrkA; Cell*(reaction_1_k1*NGF*TrkA - reaction_1_k2*NGF_TrkA);
  reaction_2: pTrkA + Akt -> pTrkA_Akt; Cell*(reaction_2_k1*pTrkA*Akt - reaction_2_k2*pTrkA_Akt);
  reaction_3: pTrkA_Akt => pTrkA + pAkt; Cell*reaction_3_k1*pTrkA_Akt;
  reaction_4: pTrkA => ; Cell*reaction_4_k1*pTrkA;
  reaction_5: pAkt + S6 -> pAkt_S6; Cell*(reaction_5_k1*pAkt*S6 - reaction_5_k2*pAkt_S6);
  reaction_6: pAkt_S6 => pAkt + pS6; Cell*reaction_6_k1*pAkt_S6;
  reaction_7: pAkt => Akt; Cell*reaction_7_k1*pAkt;
  reaction_8: pS6 => S6; Cell*reaction_8_k1*pS6;
  reaction_9: $pro_TrkA => TrkA; Cell*TrkA_turnover*pro_TrkA;
  reaction_10: NGF_TrkA => pTrkA; Cell*reaction_10_k1*NGF_TrkA;
  reaction_11: TrkA => ; Cell*TrkA_turnover*TrkA;
  NGF has ng_per_ml;

  // Species initializations:
  TrkA = pro_TrkA;
  pro_TrkA = 8.52065090518276;
  pTrkA = 0;
  pTrkA_Akt = 0;
  Akt = 1.15594897919397;
  pAkt = 0;
  S6 = 3.552336039555;
  pAkt_S6 = 0;
  pS6 = 0;
  NGF_TrkA = 0;

  // Compartment initializations:
  Cell = 1;

  // Variable initializations:
  NGF_conc_step = 0;
  NGF_conc_step has ng_per_ml;
  NGF_conc_pulse = 0;
  NGF_conc_pulse has ng_per_ml;
  pulse_time = 60;
  pulse_time has time_unit;
  NGF_conc_ramp = 30;
  NGF_conc_ramp has ng_per_ml;
  ramp_time = 3600;
  ramp_time has time_unit;
  pTrkA_total has ng_per_ml;
  pTrkA_scaleFactor = 0.848783474941268;
  pTrkA_scaleFactor has ng;
  pAkt_total has ng_per_ml;
  pAkt_scaleFactor = 2.42381211094508;
  pAkt_scaleFactor has ng;
  pS6_scaleFactor = 0.525842718263069;
  pS6_scaleFactor has ng;
  pS6_total has ng_per_ml;
  TrkA_turnover = 0.0011032440769796;
  TrkA_turnover has per_sec;
  reaction_1_k1 = 0.00269408;
  reaction_1_k2 = 0.0133747;
  reaction_2_k1 = 0.0882701;
  reaction_2_k1 has per_conc_per_sec;
  reaction_2_k2 = 1.47518e-010;
  reaction_2_k2 has per_sec;
  reaction_3_k1 = 0.0202517;
  reaction_4_k1 = 0.0684084;
  reaction_4_k1 has per_sec;
  reaction_5_k1 = 68.3666;
  reaction_5_k1 has per_conc_per_sec;
  reaction_5_k2 = 5.23519;
  reaction_5_k2 has per_sec;
  reaction_6_k1 = 0.0056515;
  reaction_6_k1 has per_sec;
  reaction_7_k1 = 1.28135;
  reaction_7_k1 has per_sec;
  reaction_8_k1 = 0.000293167;
  reaction_8_k1 has per_sec;
  reaction_10_k1 = 0.00833178;
  reaction_10_k1 has per_sec;

  // Other declarations:
  var pTrkA_total, pAkt_total, pS6_total;
  const Cell, NGF_conc_step, NGF_conc_pulse, pulse_time, NGF_conc_ramp, ramp_time;
  const pTrkA_scaleFactor, pAkt_scaleFactor, pS6_scaleFactor, TrkA_turnover;

  // Unit definitions:
  unit substance = dimensionless;
  unit conc = dimensionless / 1e-3 litre;
  unit time_unit = second;
  unit volume = 1e-3 litre;
  unit per_sec = 1 / second;
  unit ng = 1e-9 gram;
  unit ng_per_ml = 1e-9 gram / 1e-3 litre;
  unit per_conc_per_sec = 1e-3 litre * dimensionless / second;

  // Display Names:
  substance is "arbitrary_amount";
  conc is "arbitrary_conc";
  time_unit is "seconds";
  volume is "ml";
  per_sec is "per second";
  per_conc_per_sec is "per conc per second";
  reaction_1 is "NGF+TrkA";
  reaction_2 is "pTrkA+Akt";
  reaction_3 is "Akt_phosphorylation";
  reaction_4 is "pTrkA_degradation";
  reaction_5 is "pAkt+S6";
  reaction_6 is "S6_phosphorylation";
  reaction_7 is "pAkt_dephospho";
  reaction_8 is "pS6_dephospho";
  reaction_9 is "TrkA_synthesis";
  reaction_10 is "TrkA_phosphorylation";
  reaction_11 is "TrkA_degradation";
end