// Created by libAntimony v2.13.0
function Constant_flux__irreversible(v)
  v;
end

Constant_flux__irreversible is "Constant flux (irreversible)"

function logistic(r, P, k)
  r*P*(1 - P/k);
end

logistic is "logistic"

function killing(a1, M1, e, a2, Fb, C, sub, h)
  a1*(M1/(M1 + e))*(a2 + e*(1 - a2)/(Fb + e))*C*sub/(h + sub);
end

killing is "killing"

function transformation(ra, T, k1, S, k2)
  ra*(T/k1)*(S/k2)*(k1 - T);
end

transformation is "transformation"

function one_mod(k, mod)
  k*mod;
end

one_mod is "one mod"

function M2(am2y, Fy, em2y, em2b, am2b, Fb)
  (am2y*Fy/(Fy + em2y))*(em2b*(1 - am2b)/(Fb + em2b) + am2b);
end

M2 is "M2"

function M1(am1y, Fy, em1y)
  am1y*Fy/(Fy + em1y);
end

M1 is "M1"


model *Abernathy2016___glioblastoma_treatment()

  // Compartments and Species:
  compartment tumor_microenvironment;
  species Tumor in tumor_microenvironment, CancerStemCell in tumor_microenvironment;
  species CytotoxicTcell in tumor_microenvironment, TGFb in tumor_microenvironment;
  species IFNy in tumor_microenvironment, MHC1 in tumor_microenvironment;
  species MHC2 in tumor_microenvironment, $Tumor_Plot in tumor_microenvironment;
  species $CSC_Plot in tumor_microenvironment, $CTL_Plot in tumor_microenvironment;

  // Assignment Rules:
  Tumor_Plot := Tumor/100000000;
  CSC_Plot := CancerStemCell/10000000;
  CTL_Plot := CytotoxicTcell/100;
  as := at_*0.1;
  es := et;
  asb := atb;
  esb := etb;
  hs := ht;
  abs_ := abt;

  // Reactions:
  tumor_growth:  => Tumor; tumor_microenvironment*logistic(r1, Tumor, k1);
  tumor_transformation: CancerStemCell => Tumor; tumor_microenvironment*transformation(ra, Tumor, k1, CancerStemCell, k2);
  tumor_killing: Tumor => ; tumor_microenvironment*killing(at_, MHC1, etb, atb, TGFb, CytotoxicTcell, Tumor, ht);
  csc_growth:  => CancerStemCell; tumor_microenvironment*logistic(r2, CancerStemCell, k2);
  csc_killing: CancerStemCell => ; tumor_microenvironment*killing(as, MHC1, esb, asb, TGFb, CytotoxicTcell, CancerStemCell, hs);
  ctl_death: CytotoxicTcell => ; tumor_microenvironment*uc*CytotoxicTcell;
  ctl_source:  => CytotoxicTcell; tumor_microenvironment*Constant_flux__irreversible(N);
  tgfb_source:  => TGFb; tumor_microenvironment*Constant_flux__irreversible(gb);
  tgfb_by_tumor:  => TGFb; tumor_microenvironment*one_mod(abt, Tumor);
  tgfb_by_csc:  => TGFb; tumor_microenvironment*one_mod(abs_, CancerStemCell);
  tgfb_decay: TGFb => ; tumor_microenvironment*ub*TGFb;
  ifny_production:  => IFNy; tumor_microenvironment*one_mod(ayc, CytotoxicTcell);
  ifny_decay: IFNy => ; tumor_microenvironment*uy*IFNy;
  mhc1_source:  => MHC1; tumor_microenvironment*Constant_flux__irreversible(gm1);
  mhc1_decay: MHC1 => ; tumor_microenvironment*um1*MHC1;
  mhc1_stimulation:  => MHC1; tumor_microenvironment*M1(am1y, IFNy, em1y);
  mhc2_production:  => MHC2; tumor_microenvironment*M2(am2y, IFNy, em2y, em2b, am2b, TGFb);
  mhc2_decay: MHC2 => ; tumor_microenvironment*um2*MHC2;

  // Species initializations:
  Tumor = 70;
  Tumor has substance_per_volume;
  CancerStemCell = 30;
  CancerStemCell has substance_per_volume;
  CytotoxicTcell = 250;
  CytotoxicTcell has substance_per_volume;
  TGFb = 50;
  TGFb has substance_per_volume;
  IFNy = 50;
  IFNy has substance_per_volume;
  MHC1 = 50;
  MHC1 has substance_per_volume;
  MHC2 = 50;
  MHC2 has substance_per_volume;
  Tumor_Plot has substance_per_volume;
  CSC_Plot has substance_per_volume;
  CTL_Plot has substance_per_volume;

  // Compartment initializations:
  tumor_microenvironment = 1;
  tumor_microenvironment has volume;

  // Variable initializations:
  r1 = 0.001;
  r1 has unit_0;
  k1 = 100000000;
  k1 has unit_1;
  at_ = 0.12;
  at_ has unit_0;
  et = 50;
  et has unit_1;
  atb = 0.69;
  atb has unit_1;
  etb = 10000;
  etb has unit_1;
  ht = 500000000;
  ht has unit_1;
  r2 = 0.1;
  r2 has unit_0;
  k2 = 10000000;
  k2 has unit_1;
  ra = 0.006;
  ra has unit_0;
  as has unit_0;
  es has unit_1;
  asb has unit_1;
  esb has unit_1;
  hs has unit_1;
  uc = 0.007;
  uc has unit_0;
  gb = 63945;
  gb has unit_0;
  abt = 5.75e-06;
  abt has unit_0;
  abs_ has unit_0;
  ub = 7;
  ub has unit_0;
  gm1 = 1.44;
  gm1 has unit_0;
  am1y = 2.88;
  am1y has unit_0;
  em1y = 338000;
  em1y has unit_1;
  um1 = 0.0144;
  um1 has unit_0;
  am2y = 8660;
  am2y has unit_0;
  em2y = 1420;
  em2y has unit_1;
  am2b = 0.012;
  am2b has unit_1;
  em2b = 100000;
  em2b has unit_1;
  um2 = 0.0144;
  um2 has unit_0;
  ayc = 0.000102;
  ayc has unit_0;
  uy = 0.102;
  uy has unit_0;
  N = 0;
  N has unit_0;

  // Other declarations:
  var as, es, asb, esb, hs, abs_;
  const tumor_microenvironment, r1, k1, at_, et, atb, etb, ht, r2, k2, ra;
  const uc, gb, abt, ub, gm1, am1y, em1y, um1, am2y, em2y, am2b, em2b, um2;
  const ayc, uy, N;

  // Unit definitions:
  unit length = metre;
  unit area = metre^2;
  unit volume = 1e-3 litre;
  unit time_unit = time_unit;
  unit substance = 1e-3 mole;
  unit unit_0 = 1 / 3600e2 second;
  unit unit_1 = 1 / dimensionless^-0;
  unit extent = substance;
  unit substance_per_volume = 1e-3 mole / 1e-3 litre;

  // Display Names:
  time_unit is "time";
  unit_0 is "1/h";
  unit_1 is "1";
  tumor_microenvironment is "tumor microenvironment";
  Tumor_Plot is "Tumor Plot";
  CSC_Plot is "CSC Plot";
  CTL_Plot is "CTL Plot";
  at_ is "at";
  abs_ is "abs";
  tumor_growth is "tumor growth";
  tumor_transformation is "tumor transformation";
  tumor_killing is "tumor killing";
  csc_growth is "csc growth";
  csc_killing is "csc killing";
  ctl_death is "ctl death";
  ctl_source is "ctl source";
  tgfb_source is "tgfb source";
  tgfb_by_tumor is "tgfb by tumor";
  tgfb_by_csc is "tgfb by csc";
  tgfb_decay is "tgfb decay";
  ifny_production is "ifny production";
  ifny_decay is "ifny decay";
  mhc1_source is "mhc1 source";
  mhc1_decay is "mhc1 decay";
  mhc1_stimulation is "mhc1 stimulation";
  mhc2_production is "mhc2 production";
  mhc2_decay is "mhc2 decay";

  // CV terms:
  tumor_microenvironment hypernym "http://identifiers.org/ncit/C94498"
  tumor_microenvironment hypernym "http://identifiers.org/ncit/C3058"
  Tumor hypernym "http://identifiers.org/cl/CL:0001064"
  CancerStemCell hypernym "http://identifiers.org/bto/BTO:0004254"
  CytotoxicTcell hypernym "http://identifiers.org/cl/CL:0000910"
  TGFb identity "http://identifiers.org/uniprot/P01137"
  IFNy identity "http://identifiers.org/uniprot/P01579"
  MHC1 hypernym "http://identifiers.org/ncit/C20706"
  MHC2 hypernym "http://identifiers.org/ncit/C20705"
  Tumor_Plot hypernym "http://identifiers.org/cl/CL:0001064"
  CSC_Plot hypernym "http://identifiers.org/bto/BTO:0004254"
  CTL_Plot hypernym "http://identifiers.org/cl/CL:0000910"
  r1 hypernym "http://identifiers.org/sbo/SBO:0000610"
  k1 hypernym "http://identifiers.org/sbo/SBO:0000661"
  at_ hypernym "http://identifiers.org/ncit/C53346"
  et hypernym "http://identifiers.org/sbo/SBO:0000193"
  atb hypernym "http://identifiers.org/sbo/SBO:0000540"
  etb hypernym "http://identifiers.org/sbo/SBO:0000193"
  ht hypernym "http://identifiers.org/sbo/SBO:0000193"
  r2 hypernym "http://identifiers.org/sbo/SBO:0000610"
  k2 hypernym "http://identifiers.org/sbo/SBO:0000661"
  ra hypernym "http://identifiers.org/ncit/C25636"
  as hypernym "http://identifiers.org/ncit/C25636"
  es hypernym "http://identifiers.org/sbo/SBO:0000193"
  asb hypernym "http://identifiers.org/sbo/SBO:0000540"
  esb hypernym "http://identifiers.org/sbo/SBO:0000193"
  hs hypernym "http://identifiers.org/sbo/SBO:0000193"
  uc hypernym "http://identifiers.org/ncit/C25636"
  gb hypernym "http://identifiers.org/ncit/C25636"
  abt hypernym "http://identifiers.org/ncit/C25636"
  abs_ hypernym "http://identifiers.org/ncit/C25636"
  ub hypernym "http://identifiers.org/ncit/C25636"
  gm1 hypernym "http://identifiers.org/ncit/C25636"
  am1y hypernym "http://identifiers.org/ncit/C25636"
  em1y hypernym "http://identifiers.org/sbo/SBO:0000193"
  um1 hypernym "http://identifiers.org/ncit/C25636"
  am2y hypernym "http://identifiers.org/ncit/C25636"
  em2y hypernym "http://identifiers.org/sbo/SBO:0000193"
  am2b hypernym "http://identifiers.org/sbo/SBO:0000540"
  em2b hypernym "http://identifiers.org/sbo/SBO:0000193"
  um2 hypernym "http://identifiers.org/ncit/C25636"
  ayc hypernym "http://identifiers.org/ncit/C25636"
  uy hypernym "http://identifiers.org/ncit/C25636"
  N hypernym "http://identifiers.org/ncit/C25636"
  tumor_growth hypernym "http://identifiers.org/go/GO:0008283"
  tumor_growth hypernym "http://identifiers.org/sbo/SBO:0000393"
  tumor_transformation hypernym "http://identifiers.org/go/GO:0048863"
  tumor_killing hypernym "http://identifiers.org/go/GO:0002419"
  tumor_killing hypernym "http://identifiers.org/sbo/SBO:0000179"
  csc_growth hypernym "http://identifiers.org/go/GO:0008283"
  csc_growth hypernym "http://identifiers.org/sbo/SBO:0000393"
  csc_killing hypernym "http://identifiers.org/sbo/SBO:0000179"
  csc_killing hypernym "http://identifiers.org/go/GO:0002419"
  ctl_death hypernym "http://identifiers.org/go/GO:0008219"
  ctl_death hypernym "http://identifiers.org/sbo/SBO:0000179"
  ctl_source hypernym "http://identifiers.org/sbo/SBO:0000393"
  ctl_source hypernym "http://identifiers.org/go/GO:0008283"
  tgfb_source hypernym "http://identifiers.org/sbo/SBO:0000393"
  tgfb_source hypernym "http://identifiers.org/go/GO:0038044"
  tgfb_by_tumor hypernym "http://identifiers.org/go/GO:0038044"
  tgfb_by_tumor hypernym "http://identifiers.org/sbo/SBO:0000393"
  tgfb_by_csc hypernym "http://identifiers.org/go/GO:0038044"
  tgfb_by_csc hypernym "http://identifiers.org/sbo/SBO:0000393"
  tgfb_decay hypernym "http://identifiers.org/sbo/SBO:0000179"
  tgfb_decay hypernym "http://identifiers.org/go/GO:0030163"
  ifny_production hypernym "http://identifiers.org/sbo/SBO:0000393"
  ifny_production hypernym "http://identifiers.org/go/GO:0072643"
  ifny_decay hypernym "http://identifiers.org/go/GO:0030163"
  ifny_decay hypernym "http://identifiers.org/sbo/SBO:0000179"
  mhc1_source hypernym "http://identifiers.org/go/GO:0009306"
  mhc1_source hypernym "http://identifiers.org/sbo/SBO:0000393"
  mhc1_decay hypernym "http://identifiers.org/sbo/SBO:0000179"
  mhc1_decay hypernym "http://identifiers.org/go/GO:0030163"
  mhc1_stimulation hypernym "http://identifiers.org/sbo/SBO:0000393"
  mhc1_stimulation hypernym "http://identifiers.org/go/GO:0009306"
  mhc2_production hypernym "http://identifiers.org/sbo/SBO:0000393"
  mhc2_production hypernym "http://identifiers.org/go/GO:0009306"
  mhc2_decay hypernym "http://identifiers.org/sbo/SBO:0000179"
  mhc2_decay hypernym "http://identifiers.org/go/GO:0030163"
end

Abernathy2016___glioblastoma_treatment is "Abernathy2016 - glioblastoma treatment"

Abernathy2016___glioblastoma_treatment description "http://identifiers.org/pubmed/27022405"
Abernathy2016___glioblastoma_treatment model_entity_is "http://identifiers.org/biomodels.db/MODEL1907240001",
                                                       "http://identifiers.org/biomodels.db/BIOMD0000000757"
Abernathy2016___glioblastoma_treatment property "http://identifiers.org/efo/0000519"
Abernathy2016___glioblastoma_treatment property "http://identifiers.org/go/GO:0002418"
Abernathy2016___glioblastoma_treatment property "http://identifiers.org/mamo/MAMO_0000046"
Abernathy2016___glioblastoma_treatment taxon "http://identifiers.org/taxonomy/9606"
