// Created by libAntimony v2.13.0
model *Model_1()

  // Compartments and Species:
  compartment Cell;
  species $EGF in Cell, EGFR in Cell, $pro_EGFR in Cell, pEGFR in Cell, pEGFR_Akt in Cell;
  species Akt in Cell, pAkt in Cell, S6 in Cell, pAkt_S6 in Cell, pS6 in Cell;
  species EGF_EGFR in Cell;

  // Assignment Rules:
  EGF := EGF_conc_step + piecewise(EGF_conc_impulse, time <= pulse_time, 0) + EGF_conc_ramp*time/ramp_time;
  pEGFR_total := (pEGFR + pEGFR_Akt)*pEGFR_scaleFactor;
  pAkt_total := (pAkt + pAkt_S6)*pAkt_scaleFactor;
  pS6_total := pS6*pS6_scaleFactor;

  // Reactions:
  reaction_1: $EGF + EGFR -> EGF_EGFR; Cell*(reaction_1_k1*EGF*EGFR - reaction_1_k2*EGF_EGFR);
  reaction_2: pEGFR + Akt -> pEGFR_Akt; Cell*(reaction_2_k1*pEGFR*Akt - reaction_2_k2*pEGFR_Akt);
  reaction_3: pEGFR_Akt => pEGFR + pAkt; Cell*reaction_3_k1*pEGFR_Akt;
  reaction_4: pEGFR => ; Cell*reaction_4_k1*pEGFR;
  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_EGFR => EGFR; Cell*EGFR_turnover*pro_EGFR;
  reaction_10: EGF_EGFR => pEGFR; Cell*reaction_10_k1*EGF_EGFR;
  reaction_11: EGFR => ; Cell*EGFR_turnover*EGFR;
  EGF has ng_per_ml;

  // Species initializations:
  EGFR = pro_EGFR;
  pro_EGFR = 68190.1837333797/Cell;
  pEGFR = 0;
  pEGFR_Akt = 0;
  Akt = 0.0433090165709309/Cell;
  pAkt = 0;
  S6 = 3.54316740542218/Cell;
  pAkt_S6 = 0;
  pS6 = 0;
  EGF_EGFR = 0;

  // Compartment initializations:
  Cell = 1;

  // Variable initializations:
  EGF_conc_step = 0;
  EGF_conc_step has ng_per_ml;
  EGF_conc_impulse = 0;
  EGF_conc_impulse has ng_per_ml;
  pulse_time = 60;
  pulse_time has time_unit;
  EGF_conc_ramp = 30;
  EGF_conc_ramp has ng_per_ml;
  ramp_time = 3600;
  ramp_time has time_unit;
  pEGFR_total has ng_per_ml;
  pEGFR_scaleFactor = 0.000181734813832032;
  pEGFR_scaleFactor has ng;
  pAkt_total has ng_per_ml;
  pAkt_scaleFactor = 60.0587507734138;
  pAkt_scaleFactor has ng;
  pS6_scaleFactor = 49886.2313741851;
  pS6_scaleFactor has ng;
  pS6_total has ng_per_ml;
  EGFR_turnover = 0.000106386129269658;
  EGFR_turnover has per_sec;
  reaction_1_k1 = 0.00673816;
  reaction_1_k2 = 0.040749;
  reaction_1_k2 has per_sec;
  reaction_2_k1 = 1.5543e-05;
  reaction_2_k1 has per_conc_per_sec;
  reaction_2_k2 = 0.00517473;
  reaction_2_k2 has per_sec;
  reaction_3_k1 = 0.0305684;
  reaction_3_k1 has per_sec;
  reaction_4_k1 = 0.0997194;
  reaction_4_k1 has per_sec;
  reaction_5_k1 = 2.10189e-06;
  reaction_5_k1 has per_conc_per_sec;
  reaction_5_k2 = 5.1794e-15;
  reaction_5_k2 has per_sec;
  reaction_6_k1 = 0.00121498;
  reaction_6_k1 has per_sec;
  reaction_7_k1 = 0.0327962;
  reaction_7_k1 has per_sec;
  reaction_8_k1 = 0.00113102;
  reaction_8_k1 has per_sec;
  reaction_10_k1 = 0.0192391;
  reaction_10_k1 has per_sec;

  // Other declarations:
  var pEGFR_total, pAkt_total, pS6_total;
  const Cell, EGF_conc_step, EGF_conc_impulse, pulse_time, EGF_conc_ramp;
  const ramp_time, pEGFR_scaleFactor, pAkt_scaleFactor, pS6_scaleFactor, EGFR_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 "EGF+EGFR";
  reaction_2 is "pEGFR+Akt";
  reaction_3 is "Akt_phosphorylation";
  reaction_4 is "pEGFR_degradation";
  reaction_5 is "pAkt+S6";
  reaction_6 is "S6_phosphorylation";
  reaction_7 is "pAkt_dephospho";
  reaction_8 is "pS6_dephospho";
  reaction_9 is "EGFR_synthesis";
  reaction_10 is "EGFR_phosphorylation";
  reaction_11 is "EGFR_degradation";

  // SBO terms:
  Cell.sboTerm = 290
  EGF.sboTerm = 252
  EGFR.sboTerm = 297
  pro_EGFR.sboTerm = 297
  pEGFR.sboTerm = 297
  pEGFR_Akt.sboTerm = 297
  Akt.sboTerm = 252
  pAkt.sboTerm = 252
  S6.sboTerm = 252
  pAkt_S6.sboTerm = 297
  pS6.sboTerm = 252
  EGF_EGFR.sboTerm = 297
  reaction_1.sboTerm = 177
  reaction_2.sboTerm = 177
  reaction_3.sboTerm = 216
  reaction_4.sboTerm = 179
  reaction_5.sboTerm = 179
  reaction_6.sboTerm = 179
  reaction_7.sboTerm = 330
  reaction_8.sboTerm = 330
  reaction_9.sboTerm = 184
  reaction_10.sboTerm = 179
  reaction_11.sboTerm = 179

  // CV terms:
  Cell hypernym "http://identifiers.org/go/GO:0005623"
  EGF hypernym "http://identifiers.org/interpro/IPR006209"
  EGFR hypernym "http://identifiers.org/uniprot/Q9WTS1"
  pro_EGFR hypernym "http://identifiers.org/uniprot/Q9WTS1"
  pEGFR hypernym "http://identifiers.org/uniprot/Q9WTS1"
  pEGFR_Akt part "http://identifiers.org/uniprot/Q9WTS1",
                 "http://identifiers.org/uniprot/Q63484"
  pEGFR_Akt version "http://identifiers.org/kegg.compound/C00562"
  Akt hypernym "http://identifiers.org/uniprot/Q63484"
  pAkt hypernym "http://identifiers.org/uniprot/Q63484"
  pAkt hypernym "http://identifiers.org/kegg.compound/C00562"
  S6 hypernym "http://identifiers.org/uniprot/P62755"
  pAkt_S6 version "http://identifiers.org/uniprot/P62755"
  pAkt_S6 version "http://identifiers.org/uniprot/Q63484",
                  "http://identifiers.org/kegg.compound/C00562"
  pS6 hypernym "http://identifiers.org/uniprot/P62755"
  pS6 hypernym "http://identifiers.org/kegg.compound/C00562"
  EGF_EGFR part "http://identifiers.org/uniprot/Q9WTS1"
  EGF_EGFR version "http://identifiers.org/uniprot/P07522"
  pEGFR_total hypernym "http://identifiers.org/kegg.compound/C00562"
  pEGFR_total version "http://identifiers.org/uniprot/Q63484"
  pAkt_total hypernym "http://identifiers.org/kegg.compound/C00562"
  pAkt_total version "http://identifiers.org/uniprot/Q63484"
  pS6_total hypernym "http://identifiers.org/kegg.compound/C00562"
  pS6_total hypernym "http://identifiers.org/uniprot/P62755"
  reaction_1 hypernym "http://identifiers.org/go/GO:0005515"
  reaction_1 hypernym "http://identifiers.org/go/GO:0005154"
  reaction_2 hypernym "http://identifiers.org/go/GO:0005515"
  reaction_3 hypernym "http://identifiers.org/go/GO:0004672"
  reaction_4 hypernym "http://identifiers.org/go/GO:0030163"
  reaction_5 hypernym "http://identifiers.org/go/GO:0005515"
  reaction_5 hypernym "http://identifiers.org/reactome/REACT_12442"
  reaction_6 hypernym "http://identifiers.org/go/GO:0004672"
  reaction_7 hypernym "http://identifiers.org/go/GO:0004721"
  reaction_8 hypernym "http://identifiers.org/go/GO:0004721"
  reaction_9 hypernym "http://identifiers.org/go/GO:0010467"
  reaction_10 hypernym "http://identifiers.org/go/GO:0004672"
  reaction_11 hypernym "http://identifiers.org/go/GO:0030163"
end

Model_1 is "Fujita2010_Akt_Signalling_EGF"

Model_1 model_entity_is "http://identifiers.org/biomodels.db/MODEL1004060001"
Model_1 model_entity_is "http://identifiers.org/biomodels.db/BIOMD0000000262"
Model_1 description "http://identifiers.org/pubmed/20664065"
Model_1 version "http://identifiers.org/kegg.pathway/rno04012",
                "http://identifiers.org/reactome/REACT_12464.1",
                "http://identifiers.org/reactome/REACT_9417.3",
                "http://identifiers.org/go/GO:0007173",
                "http://identifiers.org/go/GO:0043491",
                "http://identifiers.org/go/GO:0071364"
Model_1 container "http://identifiers.org/bto/BTO:0001009"
Model_1 taxon "http://identifiers.org/taxonomy/10116"
