// Created by libAntimony v2.13.0
function function_for_naive_activation(naive, CML, eta, k)
  k*naive*(CML/(CML + eta));
end

function_for_naive_activation is "function for naive activation"

function function_for_T_cell_effector_death_by_CML(param, CML, effector)
  param*CML*effector;
end

function_for_T_cell_effector_death_by_CML is "function for T_cell_effector death by CML"

function function_for_CML_growth(r, C, Cmax)
  r*C*ln(Cmax/C);
end

function_for_CML_growth is "function for CML growth"

function function_for_CML_death_by_T_cell_effector(param, mod, substrate)
  param*mod*substrate;
end

function_for_CML_death_by_T_cell_effector is "function for CML death by T_cell_effector"

function function_for_T_cell_effector_production_from_T_cell_naive_activation(alpha, k, naive, CML, eta)
  alpha*k*naive*(CML/(CML + eta));
end

function_for_T_cell_effector_production_from_T_cell_naive_activation is "function for T_cell_effector production from T_cell_naive activation"

function function_for_T_cell_effector_recruitment(alpha, effector, CML, eta)
  alpha*effector*(CML/(CML + eta));
end

function_for_T_cell_effector_recruitment is "function for T_cell_effector_recruitment"


model *Moore2004_CML_TcellInteration()

  // Compartments and Species:
  compartment COMpartment;
  species CML in COMpartment, T_cell_naive in COMpartment, T_cell_effector in COMpartment;
  species $Source in COMpartment, $Sink in COMpartment;

  // Reactions:
  T_cell_naive_Source: $Source => T_cell_naive; COMpartment*sn*Source;
  T_cell_naive_Natural_Death: T_cell_naive => $Sink; COMpartment*dn*T_cell_naive;
  T_cell_naive_Activation: T_cell_naive => $Sink; COMpartment*function_for_naive_activation(T_cell_naive, CML, eta, kn);
  T_cell_effector_Recruitment: $Source => T_cell_effector; COMpartment*function_for_T_cell_effector_recruitment(alpha_e, T_cell_effector, CML, eta);
  T_cell_effector_Natural_Death: T_cell_effector => $Sink; COMpartment*de*T_cell_effector;
  T_cell_effector_Death_by_CML: T_cell_effector => $Sink; COMpartment*function_for_T_cell_effector_death_by_CML(gamma_e, CML, T_cell_effector);
  CML_Growth: $Source => CML; COMpartment*function_for_CML_growth(rc, CML, Cmax);
  CML_death_by_T_cell_effector: CML => $Sink; COMpartment*function_for_CML_death_by_T_cell_effector(gamma_c, T_cell_effector, CML);
  CML_natural_death: CML => $Sink; COMpartment*dc*CML;
  T_cell_effector_Production_from_T_cell_Naive_activation: $Source => T_cell_effector; COMpartment*function_for_T_cell_effector_production_from_T_cell_naive_activation(alpha_n, kn, T_cell_naive, CML, eta);

  // Species initializations:
  CML = 10000;
  T_cell_naive = 1510;
  T_cell_effector = 20;
  Source = 1;
  Sink = 1;

  // Compartment initializations:
  COMpartment = 1;

  // Variable initializations:
  sn = 0.071;
  sn has unit_0;
  dn = 0.05;
  dn has unit_1;
  alpha_n = 0.56;
  alpha_n has unit_2;
  alpha_e = 0.53;
  alpha_e has unit_1;
  de = 0.12;
  de has unit_1;
  gamma_e = 0.0077;
  gamma_e has unit_3;
  Cmax = 190000;
  Cmax has unit_4;
  rc = 0.23;
  rc has unit_1;
  dc = 0.68;
  dc has unit_1;
  gamma_c = 0.047;
  gamma_c has unit_3;
  kn = 0.063;
  kn has unit_1;
  eta = 43;
  eta has unit_4;

  // Other declarations:
  const COMpartment, sn, dn, alpha_n, alpha_e, de, gamma_e, Cmax, rc, dc;
  const gamma_c, kn, eta;

  // Unit definitions:
  unit time_unit = 86400 second;
  unit substance = item;
  unit unit_0 = 1 / (11.5741 litre * second);
  unit unit_1 = 1 / 0.0115741e-3 second;
  unit unit_2 = 1 / dimensionless^-0;
  unit unit_3 = 0.0864 litre / second;
  unit unit_4 = 1 / 1e6 litre;

  // Display Names:
  time_unit is "time";
  unit_0 is "1/(11.5741*l*s)";
  unit_1 is "1/(0.0115741*ms)";
  unit_2 is "1";
  unit_3 is "0.0864*l/s";
  unit_4 is "1/Ml";
  COMpartment is "Blood";
  T_cell_naive_Source is "T_cell_naive Source";
  T_cell_naive_Natural_Death is "T_cell_naive Natural Death";
  T_cell_naive_Activation is "T_cell_naive Activation";
  T_cell_effector_Recruitment is "T_cell_effector Recruitment";
  T_cell_effector_Natural_Death is "T_cell_effector Natural Death";
  T_cell_effector_Death_by_CML is "T_cell_effector Death by CML";
  CML_Growth is "CML Growth";
  CML_death_by_T_cell_effector is "CML death by T_cell_effector";
  CML_natural_death is "CML natural death";
  T_cell_effector_Production_from_T_cell_Naive_activation is "T_cell_effector Production from T_cell_Naive activation";

  // CV terms:
  COMpartment hypernym "http://identifiers.org/bto/BTO:0001102"
  CML hypernym "http://identifiers.org/bto/BTO:0001271"
  T_cell_naive hypernym "http://identifiers.org/ncit/C104081"
  T_cell_effector hypernym "http://identifiers.org/ncit/C104083"
  alpha_n description "http://identifiers.org/isbn/081533642X"
  de description "http://identifiers.org/pubmed/8186756"
  rc description "http://identifiers.org/pubmed/10812720"
  dc description "http://identifiers.org/pubmed/5239861"
  gamma_c description "http://identifiers.org/doi/10.1006/jtbi.1994.1199"
  kn description "http://identifiers.org/doi/10.1006/jtbi.1994.1199"
  T_cell_naive_Source hypernym "http://identifiers.org/ncit/C25683"
  T_cell_naive_Natural_Death hypernym "http://identifiers.org/go/GO:0008219"
  T_cell_naive_Activation hypernym "http://identifiers.org/go/GO:0042110"
  T_cell_effector_Recruitment hypernym "http://identifiers.org/go/GO:0050778"
  T_cell_effector_Natural_Death hypernym "http://identifiers.org/go/GO:0008219"
  T_cell_effector_Death_by_CML hypernym "http://identifiers.org/ncit/GO:0070241"
  CML_Growth hypernym "http://identifiers.org/ncit/C19387"
  CML_death_by_T_cell_effector hypernym "http://identifiers.org/go/GO:0008219"
  CML_natural_death hypernym "http://identifiers.org/go/GO:0008219"
  T_cell_effector_Production_from_T_cell_Naive_activation hypernym "http://identifiers.org/go/GO:0042110"
end

Moore2004_CML_TcellInteration is "Moore2004 - Chronic Myeloid Leukemic cells and T-lymphocyte interaction"

Moore2004_CML_TcellInteration model_entity_is "http://identifiers.org/biomodels.db/MODEL1006230057"
Moore2004_CML_TcellInteration unknown_model_qual "http://identifiers.org/mamo/MAMO_0000046"
Moore2004_CML_TcellInteration description "http://identifiers.org/pubmed/15038986"
Moore2004_CML_TcellInteration model_entity_is "http://identifiers.org/biomodels.db/BIOMD0000000662"
Moore2004_CML_TcellInteration hypernym "http://identifiers.org/efo/0000339"
Moore2004_CML_TcellInteration property "http://identifiers.org/go/GO:0002262"
Moore2004_CML_TcellInteration taxon "http://identifiers.org/taxonomy/9606"
