// Created by libAntimony v2.13.0
model *Xie2007_CircClock()

  // Compartments and Species:
  compartment wholeCell;
  species CC in wholeCell, CCPT in wholeCell, clkp in wholeCell, perp in wholeCell;
  species clkm in wholeCell, perm in wholeCell, PT in wholeCell, vrip in wholeCell;
  species vrim in wholeCell, VRI in wholeCell, pdpp in wholeCell, pdpm in wholeCell;
  species PDP in wholeCell, CLK in wholeCell, PER in wholeCell, timp in wholeCell;
  species timm in wholeCell, TIM in wholeCell, $CYC in wholeCell, prcper in wholeCell;
  species prcv in wholeCell, prcpdp in wholeCell, prvc in wholeCell, prpc in wholeCell;
  species prct in wholeCell;

  // Reactions:
  re1: CC + PT => CCPT; wholeCell*CC*PT*bccpt;
  re2: CC => ; wholeCell*CC*dcc;
  re3: CCPT => ; wholeCell*CCPT*dccpt;
  re4: PT => ; wholeCell*PT*dpt;
  re9: clkm => ; wholeCell*clkm*dclkm;
  re10:  => CLK; wholeCell*clkm*tlclk;
  re15: perm => ; wholeCell*perm*dperm;
  re17:  => PER; wholeCell*perm*tlper;
  re20:  => perm; wholeCell*((1 - (1 - prcper)^npt)*tcccperp + (1 - prcper)^npt*tcdvpmt)*perp;
  re28:  => vrim; wholeCell*((1 - (1 - prcv)^nvri)*tcccvrip + (1 - prcv)^nvri*tcdvpmt)*vrip;
  re30: vrim => ; wholeCell*vrim*dvrim;
  re31:  => VRI; wholeCell*vrim*tlvri;
  re32: VRI => ; wholeCell*VRI*dvri;
  re35:  => pdpm; wholeCell*((1 - (1 - prcpdp)^npdp)*tcccpdpp + (1 - prcpdp)^npdp*tcdvpmt)*pdpp;
  re37: pdpm => ; wholeCell*pdpm*dpdpm;
  re38:  => PDP; wholeCell*pdpm*tlpdp;
  re39: PDP => ; wholeCell*PDP*dpdp;
  re42:  => clkm; wholeCell*(prvc*tcvriclkp + prpc*tcpdpclkp + (1 - prvc - prpc)*tcclkp)*clkp;
  re43: CLK + $CYC => CC; wholeCell*CLK*bcc*CYC;
  re44: CLK => ; wholeCell*CLK*dclk;
  re45: CC => CLK + $CYC; wholeCell*CC*ubcc;
  re46: PER + TIM => PT; wholeCell*PER*TIM*bpt;
  re47: PT => PER + TIM; wholeCell*PT*ubpt;
  re48: PER => ; wholeCell*PER*dper;
  re51:  => timm; wholeCell*((1 - (1 - prct)^npt)*tccctimp + (1 - prct)^npt*tcdvpmt)*timp;
  re53: timm => ; wholeCell*timm*dtimm;
  re54:  => TIM; wholeCell*timm*tltim;
  re55: TIM => ; wholeCell*TIM*dtim;
  re56: CCPT => CC + PT; wholeCell*CCPT*ubccpt;
  re57:  => prcper; wholeCell*(1 - prcper)*bccperp*CC;
  re58: prcper => ; wholeCell*prcper*ubccperp;
  re59: prcv => ; wholeCell*ubccvrip*prcv;
  re60:  => prcv; wholeCell*(1 - prcv)*bccvrip*CC;
  re61: prcpdp => ; wholeCell*ubccpdpp*prcpdp;
  re62:  => prcpdp; wholeCell*(1 - prcpdp)*bccpdpp*CC;
  re63:  => prvc; wholeCell*(1 - prvc - prpc)*bvriclkp*VRI;
  re64: prvc => ; wholeCell*prvc*ubvriclkp;
  re65:  => prpc; wholeCell*(1 - prvc - prpc)*bpdpclkp*PDP;
  re66: prpc => ; wholeCell*prpc*ubpdpclkp;
  re68:  => prct; wholeCell*(1 - prct)*bcctimp*CC;
  re69: prct => ; wholeCell*prct*ubcctimp;

  // Species initializations:
  CC = 0.5566;
  CCPT = 0.4982;
  clkp = 0.003185;
  perp = 0.003185;
  clkm = 0.2583;
  perm = 0.2395;
  PT = 0.4014;
  vrip = 0.003185;
  vrim = 0.2571;
  VRI = 3.175;
  pdpp = 0.003185;
  pdpm = 0.3175;
  PDP = 4.1953;
  CLK = 3.6628;
  PER = 2.7527;
  timp = 0.003185;
  timm = 0.2395;
  TIM = 2.7527;
  CYC = 1;
  prcper = 0.0431/wholeCell;
  prcv = 0.0585/wholeCell;
  prcpdp = 0.08/wholeCell;
  prvc = 0.489/wholeCell;
  prpc = 0.426/wholeCell;
  prct = 0.043/wholeCell;

  // Compartment initializations:
  wholeCell = 1;

  // Variable initializations:
  dccpt = 15.06;
  bccperp = 0.069;
  ubccperp = 0.262;
  bccpt = 51;
  dperm = 0.053;
  tlper = 36;
  tcccperp = 11;
  tcdvpmt = 0.028;
  dvri = 1.226;
  tcclkp = 1.42;
  bcc = 2.349;
  dclk = 0.2;
  ubcc = 0.89;
  bpt = 1.1;
  ubpt = 2.93;
  dper = 0.62;
  tcccvrip = 16.86;
  tcccpdpp = 9.831;
  dvrim = 0.07;
  dpdpm = 0.06;
  ubccpt = 7.89;
  tlvri = 14.68;
  tlpdp = 1.87;
  bccvrip = 0.1;
  bccpdpp = 0.062;
  ubccvrip = 0.276;
  ubccpdpp = 0.145;
  tcpdpclkp = 125.54;
  dclkm = 0.643;
  bvriclkp = 1.858;
  bpdpclkp = 1.155;
  ubvriclkp = 1.043;
  ubpdpclkp = 0.952;
  tcvriclkp = 0.053;
  dpdp = 0.156;
  tlclk = 35;
  dcc = 0.184;
  dpt = 0.279;
  dtim = 0.62;
  dtimm = 0.053;
  tltim = 36;
  bcctimp = 0.069;
  ubcctimp = 0.262;
  tccctimp = 11;
  npt = 5;
  nvri = 4;
  npdp = 6;

  // Other declarations:
  const wholeCell, dccpt, bccperp, ubccperp, bccpt, dperm, tlper, tcccperp;
  const tcdvpmt, dvri, tcclkp, bcc, dclk, ubcc, bpt, ubpt, dper, tcccvrip;
  const tcccpdpp, dvrim, dpdpm, ubccpt, tlvri, tlpdp, bccvrip, bccpdpp, ubccvrip;
  const ubccpdpp, tcpdpclkp, dclkm, bvriclkp, bpdpclkp, ubvriclkp, ubpdpclkp;
  const tcvriclkp, dpdp, tlclk, dcc, dpt, dtim, dtimm, tltim, bcctimp, ubcctimp;
  const tccctimp, npt, nvri, npdp;

  // Unit definitions:
  unit substance = 1e-9 mole;
  unit time_unit = 3600 second;

  // Display Names:
  substance is "nano mole";
  time_unit is "hour";
  prcper is "CCbindingPer";
  prcv is "CCbindingvri";
  prcpdp is "CCbindingpdp";
  prvc is "VRIbindingclkp";
  prpc is "PDPbindingclkp";
  prct is "CCbindingtim";
  re1 is "CC PT association";
  re2 is "Degradation of CLK CYK dimer";
  re3 is "Degradation of CC PT dimer";
  re4 is "Degradation of PER TIM dimer";
  re9 is "Degradation of clk mRNA";
  re10 is "clkm translation";
  re15 is "Degradation of per mRNA";
  re17 is "perm translation";
  re20 is "per transcription";
  re28 is "vri transcription";
  re30 is "Degradation of vri mRNA";
  re31 is "vrim translation";
  re32 is "VRI protein degradation";
  re35 is "pdp transcription";
  re37 is "Degradation of pdp mRNA";
  re38 is "pdpm translation";
  re39 is "PDP protein degradation";
  re42 is "clk transcription";
  re43 is "CLK CYC association";
  re44 is "CLK protein degradation";
  re45 is "CLK CYC dissociation";
  re46 is "PER TIM association";
  re47 is "PER TIM dissociation";
  re48 is "PER protein degradation";
  re51 is "tim transcription";
  re53 is "Degradation of tim mRNA";
  re54 is "timm translation";
  re55 is "TIM protein degradation";
  re56 is "CC PT dimer dissociation";
  re57 is "CC binding probability in per promoter";
  re58 is "CC Unbinding probability in per promoter";
  re59 is "CC Unbinding probability in vri promoter";
  re60 is "CC binding probability in vri promoter";
  re61 is "CC Unbinding probability in pdp1 promoter";
  re62 is "CC binding probability in pdp1 promoter";
  re63 is "VRI binding clk promoter";
  re64 is "VRI unbinding clk promoter";
  re65 is "PDP binding clk promoter";
  re66 is "PDP unbinding clk promoter";
  re68 is "CC binding probability in tim promoter";
  re69 is "CC Unbinding probability in tim promoter";

  // CV terms:
  wholeCell identity "http://identifiers.org/obo.go/GO:0005623"
  CC part "http://identifiers.org/uniprot/O61734",
          "http://identifiers.org/uniprot/O61735"
  CCPT part "http://identifiers.org/uniprot/Q59E16",
            "http://identifiers.org/uniprot/P07663",
            "http://identifiers.org/uniprot/O61734",
            "http://identifiers.org/uniprot/O61735"
  PT part "http://identifiers.org/uniprot/Q59E16",
          "http://identifiers.org/uniprot/P07663"
  VRI identity "http://identifiers.org/uniprot/Q9VMS4"
  PDP hypernym "http://identifiers.org/uniprot/Q9TW49"
  CLK hypernym "http://identifiers.org/uniprot/O61735"
  PER hypernym "http://identifiers.org/uniprot/P07663"
  TIM hypernym "http://identifiers.org/uniprot/Q59E16"
  CYC hypernym "http://identifiers.org/uniprot/O61734"
  re1 hypernym "http://identifiers.org/obo.go/GO:0046982"
  re2 hypernym "http://identifiers.org/obo.go/GO:0044257"
  re3 hypernym "http://identifiers.org/obo.go/GO:0044257"
  re4 hypernym "http://identifiers.org/obo.go/GO:0044257"
  re9 hypernym "http://identifiers.org/obo.go/GO:0006402"
  re10 hypernym "http://identifiers.org/obo.go/GO:0006412"
  re15 hypernym "http://identifiers.org/obo.go/GO:0006402"
  re17 hypernym "http://identifiers.org/obo.go/GO:0006412"
  re20 hypernym "http://identifiers.org/obo.go/GO:0006351"
  re28 hypernym "http://identifiers.org/obo.go/GO:0006351"
  re30 hypernym "http://identifiers.org/obo.go/GO:0006402"
  re31 hypernym "http://identifiers.org/obo.go/GO:0006412"
  re32 hypernym "http://identifiers.org/obo.go/GO:0044257"
  re35 hypernym "http://identifiers.org/obo.go/GO:0006351"
  re37 hypernym "http://identifiers.org/obo.go/GO:0006402"
  re38 hypernym "http://identifiers.org/obo.go/GO:0006412"
  re39 hypernym "http://identifiers.org/obo.go/GO:0044257"
  re42 hypernym "http://identifiers.org/obo.go/GO:0006351"
  re43 hypernym "http://identifiers.org/obo.go/GO:0046982"
  re44 hypernym "http://identifiers.org/obo.go/GO:0044257"
  re45 hypernym "http://identifiers.org/obo.go/GO:0043624"
  re46 hypernym "http://identifiers.org/obo.go/GO:0046982"
  re47 hypernym "http://identifiers.org/obo.go/GO:0043624"
  re48 hypernym "http://identifiers.org/obo.go/GO:0044257"
  re51 hypernym "http://identifiers.org/obo.go/GO:0006351"
  re53 hypernym "http://identifiers.org/obo.go/GO:0006402"
  re54 hypernym "http://identifiers.org/obo.go/GO:0006412"
  re55 hypernym "http://identifiers.org/obo.go/GO:0044257"
  re56 hypernym "http://identifiers.org/obo.go/GO:0046982"
  re57 hypernym "http://identifiers.org/obo.go/GO:0006357"
  re58 hypernym "http://identifiers.org/obo.go/GO:0006357"
  re59 hypernym "http://identifiers.org/obo.go/GO:0006357"
  re60 hypernym "http://identifiers.org/obo.go/GO:0006357"
  re61 hypernym "http://identifiers.org/obo.go/GO:0006357"
  re62 hypernym "http://identifiers.org/obo.go/GO:0006357"
  re63 hypernym "http://identifiers.org/obo.go/GO:0030528"
  re64 hypernym "http://identifiers.org/obo.go/GO:0030528"
  re65 hypernym "http://identifiers.org/obo.go/GO:0003700"
  re66 hypernym "http://identifiers.org/obo.go/GO:0043433"
  re68 hypernym "http://identifiers.org/obo.go/GO:0006357"
  re69 hypernym "http://identifiers.org/obo.go/GO:0006357"
end

Xie2007_CircClock is "Xie2007_CircClock"

Xie2007_CircClock model_entity_is "http://identifiers.org/biomodels.db/MODEL1029395046"
Xie2007_CircClock model_entity_is "http://identifiers.org/biomodels.db/BIOMD0000000160"
Xie2007_CircClock description "http://identifiers.org/pubmed/17157878"
Xie2007_CircClock taxon "http://identifiers.org/taxonomy/7227"
Xie2007_CircClock parthood "http://identifiers.org/kegg.pathway/dme04711"
Xie2007_CircClock identity "http://identifiers.org/obo.go/GO:0007623",
                           "http://identifiers.org/obo.go/GO:0045187"
