// Created by libAntimony v2.13.0
function Function_for_Si_Proliferation(pSi, Si, N, Mi)
  pSi*Si*(1 - Si/(Si + N*Mi));
end

Function_for_Si_Proliferation is "Function_for_Si_Proliferation"

function Function_for_Mi_Lysis_Si(lMi, CD4, CD8, Mi, cCD4CD8)
  lMi*(CD4 + CD8/Mi)/(CD4 + CD8/Mi + cCD4CD8);
end

Function_for_Mi_Lysis_Si is "Function_for_Mi_Lysis_Si"

function Function_for_CD8_Growth_Boost(gbCD8, CD8, cc1CD8, k2CD8)
  gbCD8*CD8*(1 - CD8/cc1CD8)*(CD8/(CD8 + k2CD8));
end

Function_for_CD8_Growth_Boost is "Function_for_CD8_Growth_Boost"

function Function_for_Mi_Lysis(lMi, CD4, CD8, Mi, cCD4CD8, apop, Si, N)
  (1 - apop*Si/(Si + N + Mi))*lMi*(CD4 + CD8/Mi)/(CD4 + CD8/Mi + cCD4CD8);
end

Function_for_Mi_Lysis is "Function_for_Mi_Lysis"

function Function_for_Mr_Infection_Si(iMr, Mr, Se, cSeMr)
  iMr*Mr*Se/(Se + cSeMr);
end

Function_for_Mr_Infection_Si is "Function_for_Mr_Infection_Si"

function Function_for_CD4_Interaction_Naive_Se(CD4n, CD4, Se, ndCD4, kSedCD4)
  CD4n*CD4*Se^ndCD4/(Se^ndCD4 + kSedCD4^ndCD4);
end

Function_for_CD4_Interaction_Naive_Se is "Function_for_CD4_Interaction_Naive_Se"

function Function_for_CD8_Competition(compCD8, CD8, Se, w1, CD4, ncompcd8, kcompCD4)
  compCD8*CD8*(Se/(Se + w1))*(CD4^ncompcd8/(CD4^ncompcd8 + kcompCD4^ncompcd8));
end

Function_for_CD8_Competition is "Function_for_CD8_Competition"

function Function_for_Mi_Bursting(bMi, Mi, Si, mMi, N)
  bMi*Mi*Si^mMi/(Si^mMi + (N*Mi)^mMi);
end

Function_for_Mi_Bursting is "Function_for_Mi_Bursting"

function Function_for_CD4_Recruitment(CD4rec, vrecCD4, Se, kmrecCD4)
  CD4rec*vrecCD4*Se/(Se + kmrecCD4);
end

Function_for_CD4_Recruitment is "Function_for_CD4_Recruitment"

function Constant_flux__irreversible(v)
  v;
end

Constant_flux__irreversible is "Constant flux (irreversible)"

function Function_for_Mr_Recruitment(Mrrec, vrecMr, Se, kmrecMr)
  Mrrec*vrecMr*Se/(Se + kmrecMr);
end

Function_for_Mr_Recruitment is "Function_for_Mr_Recruitment"

function Function_for_Mr_Infection(iMr, Mr, Se, cSeMri)
  iMr*Mr*Se/(Se + cSeMri);
end

Function_for_Mr_Infection is "Function_for_Mr_Infection"

function Function_for_Mr_Growth_Boost(Mr, ccMr, p1, gbMr)
  gbMr*Mr*(1 - Mr/(ccMr - ccMr*p1));
end

Function_for_Mr_Growth_Boost is "Function_for_Mr_Growth_Boost"

function Function_for_Mr_Activation(aMr, Mr, Se, cSeMr)
  aMr*Mr*Se/(Se + cSeMr);
end

Function_for_Mr_Activation is "Function_for_Mr_Activation"

function Function_for_CD4_Growth_Boost(gbCD4, CD4, cc1CD4, ngbCD4, k2CD4)
  gbCD4*CD4*(1 - CD4/cc1CD4)*(CD4^ngbCD4/(CD4^ngbCD4 + k2CD4^ngbCD4));
end

Function_for_CD4_Growth_Boost is "Function_for_CD4_Growth_Boost"

function Function_for_Se_Proliferation(pSe, Se, ccSe)
  pSe*Se*(1 - Se/ccSe);
end

Function_for_Se_Proliferation is "Function_for_Se_Proliferation"

function Function_for_Ma_Deactivation(daMa, Ma, CD4, cdaMA)
  daMa*Ma*CD4/(CD4 + cdaMA);
end

Function_for_Ma_Deactivation is "Function_for_Ma_Deactivation"


model *Schokker2013___A_mathematical_model_representing_cellular_immune_development_and_response_to_Salmonella_of_chicken_intestinal_tissue()

  // Compartments and Species:
  compartment compartment_;
  species CD4 in compartment_, CD8 in compartment_, Mr in compartment_, Ma in compartment_;
  species Mi in compartment_, Se in compartment_, Si in compartment_, CD4rec in compartment_;
  species Mrrec in compartment_;

  // Reactions:
  Mr_Source:  => Mr; compartment_*Constant_flux__irreversible(sMr);
  Mr_Growth_Boost:  => Mr; compartment_*Function_for_Mr_Growth_Boost(Mr, ccMr, p1, gbMr);
  Mr_Recruitment: Mrrec => Mr; compartment_*Function_for_Mr_Recruitment(Mrrec, vrecMr, Se, kmrecMr);
  Ma_Deactivation: Ma => Mr; compartment_*Function_for_Ma_Deactivation(daMa, Ma, CD4, cdaMa);
  Mr_Infection: Mr + Se => Mi; compartment_*Function_for_Mr_Infection(iMr, Mr, Se, cSeMri);
  Mr_Activation: Mr => Ma; compartment_*Function_for_Mr_Activation(aMr, Mr, Se, cSeMr);
  Se_Killing_Mr: Mr + Se => ; compartment_*kSeMr*Mr*Se;
  Mr_Death: Mr => ; compartment_*drMr*Mr;
  CD4_Source:  => CD4; compartment_*Constant_flux__irreversible(sCD4);
  CD4_Growth_Boost:  => CD4; compartment_*Function_for_CD4_Growth_Boost(gbCD4, CD4, cc1CD4, ngbCD4, k2CD4);
  CD4_Recruitment: CD4rec => CD4; compartment_*Function_for_CD4_Recruitment(CD4rec, vrecCD4, Se, kmrecCD4);
  Se_Killing_CD4: CD4 + Se => ; compartment_*kSeCD4*CD4*Se;
  CD4_Interaction_Naive_Se: CD4 => ; compartment_*Function_for_CD4_Interaction_Naive_Se(CD4n, CD4, Se, ndCD4, kSedCD4);
  CD4_Death: CD4 => ; compartment_*drCD4*CD4;
  CD8_Source:  => CD8; compartment_*Constant_flux__irreversible(sCD8);
  CD8_Growth_Boost:  => CD8; compartment_*Function_for_CD8_Growth_Boost(gbCD8, CD8, cc1CD8, k2CD8);
  CD8_Competition: CD8 => ; compartment_*Function_for_CD8_Competition(compCD8, CD8, Se, w1, CD4, ncompCD4, kcompCD4);
  CD8_Death: CD8 => ; compartment_*drCD8*CD8;
  Ma_Death: Ma => ; compartment_*drMa*Ma;
  Se_Killing_Ma: Ma + Se => ; compartment_*kSeMa*Ma*Se;
  Mi_Bursting: Si + Mi => Se; compartment_*Function_for_Mi_Bursting(bMi, Mi, Si, mMi, N);
  Mi_Lysis: Mi => ; compartment_*Function_for_Mi_Lysis(lMi, CD4, CD8, Mi, cCD4CD8, apop, Si, N);
  Mi_Death: Mi => ; compartment_*drMi*Mi;
  Se_Proliferation:  => Se; compartment_*Function_for_Se_Proliferation(pSe, Se, ccSe);
  Se_Death: Se => ; compartment_*drSe*Se;
  Si_Death: Si => ; compartment_*drSi*Si;
  Si_Proliferation:  => Si; compartment_*Function_for_Si_Proliferation(pSi, Si, N, Mi);
  Mr_Infection_Si:  => Si; compartment_*Function_for_Mr_Infection_Si(iMr, Mr, Si, cSeMr);
  Mi_Lysis_Si: Si => ; compartment_*Function_for_Mi_Lysis_Si(lMi, CD4, CD8, Mi, cCD4CD8);

  // Species initializations:
  CD4 = 9000000;
  CD8 = 7000000;
  Mr = 9000000;
  Ma = 0;
  Mi = 100;
  Se = 200;
  Si = 100;
  CD4rec = 27000000;
  Mrrec = 20000000;

  // Compartment initializations:
  compartment_ = 1;

  // Variable initializations:
  sMr = 300000;
  drMr = 0.011;
  aMr = 100;
  cSeMr = 1;
  iMr = 0.1;
  cSeMri = 600000;
  kSeMr = 5e-08;
  gbMr = 1.2;
  ccMr = 25000000;
  p1 = 0.65;
  vrecMr = 1;
  kmrecMr = 1000;
  drMa = 0.08;
  kSeMa = 2.6e-07;
  daMa = 40;
  cdaMa = 30000000;
  N = 30;
  bMi = 0.4;
  mMi = 2;
  lMi = 0.8;
  cCD4CD8 = 10;
  apop = 0.7;
  drMi = 0.011;
  sCD4 = 490000;
  drCD4 = 0.016;
  gbCD4 = 0.19;
  cc1CD4 = 82000000;
  ngbCD4 = 2;
  k2CD4 = 8700000;
  kmrecCD4 = 1;
  vrecCD4 = 100;
  CD4n = 0.4;
  ndCD4 = 8;
  kSedCD4 = 4200;
  kSeCD4 = 1e-09;
  drCD8 = 0.001;
  sCD8 = 430000;
  gbCD8 = 1.44;
  cc1CD8 = 13000000;
  k2CD8 = 47000000;
  ncompCD4 = 0.5;
  kcompCD4 = 34000000;
  compCD8 = 0.85;
  w1 = 1e-25;
  drSe = 27.8;
  pSe = 35;
  ccSe = 500000;
  drSi = 0.05;
  pSi = 4.1;

  // Other declarations:
  const compartment_, sMr, drMr, aMr, cSeMr, iMr, cSeMri, kSeMr, gbMr, ccMr;
  const p1, vrecMr, kmrecMr, drMa, kSeMa, daMa, cdaMa, N, bMi, mMi, lMi, cCD4CD8;
  const apop, drMi, sCD4, drCD4, gbCD4, cc1CD4, ngbCD4, k2CD4, kmrecCD4, vrecCD4;
  const CD4n, ndCD4, kSedCD4, kSeCD4, drCD8, sCD8, gbCD8, cc1CD8, k2CD8, ncompCD4;
  const kcompCD4, compCD8, w1, drSe, pSe, ccSe, drSi, pSi;

  // Unit definitions:
  unit volume = 1e-3 litre;
  unit substance = item;
  unit time_unit = 86400 second;

  // Display Names:
  time_unit is "time";
  compartment_ is "compartment";

  // CV terms:
  compartment_ container "http://identifiers.org/ncit/C34082"
  CD4 identity "http://identifiers.org/cl/CL:0000492"
  CD8 identity "http://identifiers.org/ncit/C12542"
  Mr identity "http://identifiers.org/cl/CL:0000864"
  Ma identity "http://identifiers.org/cl/CL:0000863"
  Mi identity "http://identifiers.org/ncit/C12558"
  Mi hypernym "http://identifiers.org/bto/BTO:0000152"
  Se identity "http://identifiers.org/ncit/C76380"
  Se container "http://identifiers.org/go/GO:0005576"
  Si identity "http://identifiers.org/ncit/C76380"
  Si property "http://identifiers.org/ncit/C28217"
  CD4rec hypernym "http://identifiers.org/cl/CL:0000492"
  Mrrec hypernym "http://identifiers.org/ncit/C12558"
  Mr_Source hypernym "http://identifiers.org/go/GO:0045123"
  Mr_Growth_Boost hypernym "http://identifiers.org/ncit/C18081"
  Mr_Recruitment hypernym "http://identifiers.org/go/GO:0045123"
  Ma_Deactivation hypernym "http://identifiers.org/ncit/C40846"
  Mr_Infection hypernym "http://identifiers.org/ncit/C2890"
  Mr_Activation identity "http://identifiers.org/go/GO:0042116"
  Se_Killing_Mr hypernym "http://identifiers.org/go/GO:0001906"
  Mr_Death hypernym "http://identifiers.org/go/GO:0008219"
  CD4_Source hypernym "http://identifiers.org/go/GO:0045123"
  CD4_Growth_Boost hypernym "http://identifiers.org/ncit/C18081"
  CD4_Recruitment hypernym "http://identifiers.org/go/GO:0045123"
  Se_Killing_CD4 hypernym "http://identifiers.org/go/GO:0001906"
  CD4_Interaction_Naive_Se part "http://identifiers.org/ncit/C97350"
  CD4_Death hypernym "http://identifiers.org/go/GO:0008219"
  CD8_Source hypernym "http://identifiers.org/go/GO:0045123"
  CD8_Growth_Boost hypernym "http://identifiers.org/ncit/C18081"
  CD8_Competition hypernym "http://identifiers.org/go/GO:0035212"
  CD8_Death hypernym "http://identifiers.org/go/GO:0008219"
  Ma_Death hypernym "http://identifiers.org/go/GO:0008219"
  Se_Killing_Ma hypernym "http://identifiers.org/go/GO:0001906"
  Mi_Bursting hypernym "http://identifiers.org/ncit/C129692"
  Mi_Lysis hypernym "http://identifiers.org/ncit/C129692"
  Mi_Death hypernym "http://identifiers.org/go/GO:0008219"
  Se_Proliferation identity "http://identifiers.org/ncit/C18081"
  Se_Death hypernym "http://identifiers.org/go/GO:0008219"
  Si_Death hypernym "http://identifiers.org/go/GO:0008219"
  Si_Proliferation identity "http://identifiers.org/ncit/C18081"
  Mr_Infection_Si hypernym "http://identifiers.org/ncit/C2890"
  Mi_Lysis_Si hypernym "http://identifiers.org/ncit/C129692"
end

Schokker2013___A_mathematical_model_representing_cellular_immune_development_and_response_to_Salmonella_of_chicken_intestinal_tissue is "Schokker2013 - A mathematical model representing cellular immune development and response to Salmonella of chicken intestinal tissue"

Schokker2013___A_mathematical_model_representing_cellular_immune_development_and_response_to_Salmonella_of_chicken_intestinal_tissue description "http://identifiers.org/pubmed/23603730"
Schokker2013___A_mathematical_model_representing_cellular_immune_development_and_response_to_Salmonella_of_chicken_intestinal_tissue model_entity_is "http://identifiers.org/biomodels.db/MODEL1912160004",
                                                                                                                                                     "http://identifiers.org/biomodels.db/BIOMD0000000895"
Schokker2013___A_mathematical_model_representing_cellular_immune_development_and_response_to_Salmonella_of_chicken_intestinal_tissue property "http://identifiers.org/ncit/C17930"
Schokker2013___A_mathematical_model_representing_cellular_immune_development_and_response_to_Salmonella_of_chicken_intestinal_tissue property "http://identifiers.org/mamo/MAMO_0000046"
Schokker2013___A_mathematical_model_representing_cellular_immune_development_and_response_to_Salmonella_of_chicken_intestinal_tissue property "http://identifiers.org/ncit/C34082"
Schokker2013___A_mathematical_model_representing_cellular_immune_development_and_response_to_Salmonella_of_chicken_intestinal_tissue property "http://identifiers.org/ncit/C157974"
Schokker2013___A_mathematical_model_representing_cellular_immune_development_and_response_to_Salmonella_of_chicken_intestinal_tissue taxon "http://identifiers.org/taxonomy/9031"
