bives 0.1

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Files changed (16) hide show
  1. checksums.yaml +15 -0
  2. data/.gitignore +18 -0
  3. data/.ruby-gemset +1 -0
  4. data/.ruby-version +1 -0
  5. data/Gemfile +7 -0
  6. data/LICENSE.txt +22 -0
  7. data/README.md +29 -0
  8. data/Rakefile +1 -0
  9. data/bives.gemspec +36 -0
  10. data/lib/bives/version.rb +3 -0
  11. data/lib/bives.rb +40 -0
  12. data/lib/jars/BiVeS-1.1.2-SNAPSHOT-fat.jar +0 -0
  13. data/test/bives_test.rb +21 -0
  14. data/test/models/potato1.xml +1819 -0
  15. data/test/models/potato2.xml +1764 -0
  16. metadata +90 -0
data/test/models/potato2.xml ADDED
@@ -0,0 +1,1764 @@
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+ <?xml version="1.0" encoding="UTF-8"?>
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+ <!-- Created by JWS2SBML on 2008/05/26 09:12:13-->
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+ <sbml xmlns="http://www.sbml.org/sbml/level2" level="2" version="1">
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+ <model name="assmus">
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+ <listOfCompartments>
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+ <compartment id="compartment" name="compartment" size="1"/>
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+ </listOfCompartments>
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+ <listOfSpecies>
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+ <species id="G1Pam" name="G1Pam" compartment="compartment" initialConcentration="30"/>
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+ <species id="ATPam" name="ATPam" compartment="compartment" initialConcentration="150"/>
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+ <species id="ADPGam" name="ADPGam" compartment="compartment" initialConcentration="100"/>
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+ <species id="PPam" name="PPam" compartment="compartment" initialConcentration="5"/>
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+ <species id="PGA3am" name="PGA3am" compartment="compartment" initialConcentration="160"/>
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+ <species id="Pam" name="Pam" compartment="compartment" initialConcentration="2000"/>
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+ <species id="xstarch" name="xstarch" compartment="compartment" initialConcentration="1000000" boundaryCondition="true" constant="true"/>
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+ <species id="ADPam" name="ADPam" compartment="compartment" initialConcentration="100"/>
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+ <species id="Glucoseam" name="Glucoseam" compartment="compartment" initialConcentration="3000"/>
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+ <species id="Glucosecyt" name="Glucosecyt" compartment="compartment" initialConcentration="150"/>
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+ <species id="G6Pam" name="G6Pam" compartment="compartment" initialConcentration="550"/>
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+ <species id="Pcyt" name="Pcyt" compartment="compartment" initialConcentration="2000"/>
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+ <species id="G6Pcyt" name="G6Pcyt" compartment="compartment" initialConcentration="500"/>
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+ <species id="G1Pcyt" name="G1Pcyt" compartment="compartment" initialConcentration="30"/>
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+ <species id="F6Pcyt" name="F6Pcyt" compartment="compartment" initialConcentration="160"/>
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+ <species id="F16BPcyt" name="F16BPcyt" compartment="compartment" initialConcentration="1"/>
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+ <species id="PEPcyt" name="PEPcyt" compartment="compartment" initialConcentration="10"/>
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+ <species id="ATPcyt" name="ATPcyt" compartment="compartment" initialConcentration="200"/>
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+ <species id="ADPcyt" name="ADPcyt" compartment="compartment" initialConcentration="180"/>
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+ <species id="PPcyt" name="PPcyt" compartment="compartment" initialConcentration="1"/>
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+ <species id="GAPcyt" name="GAPcyt" compartment="compartment" initialConcentration="1"/>
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+ <species id="DHAPcyt" name="DHAPcyt" compartment="compartment" initialConcentration="5"/>
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+ <species id="PGA3cyt" name="PGA3cyt" compartment="compartment" initialConcentration="150"/>
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+ <species id="PGA2cyt" name="PGA2cyt" compartment="compartment" initialConcentration="20"/>
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+ <species id="xpyruvate" name="xpyruvate" compartment="compartment" initialConcentration="10" boundaryCondition="true" constant="true"/>
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+ <species id="UTPcyt" name="UTPcyt" compartment="compartment" initialConcentration="20"/>
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+ <species id="UDPGcyt" name="UDPGcyt" compartment="compartment" initialConcentration="870"/>
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+ <species id="Sucrose" name="Sucrose" compartment="compartment" initialConcentration="88000"/>
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+ <species id="UDPcyt" name="UDPcyt" compartment="compartment" initialConcentration="10"/>
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+ <species id="Fructose" name="Fructose" compartment="compartment" initialConcentration="20"/>
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+ <species id="xsucrose" name="xsucrose" compartment="compartment" initialConcentration="90000" boundaryCondition="true" constant="true"/>
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+ </listOfSpecies>
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+ <listOfParameters>
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+ <parameter id="VmaxAGPase" name="VmaxAGPase" value="312"/>
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+ <parameter id="KmG1PAGPase" name="KmG1PAGPase" value="100"/>
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+ <parameter id="KmATPAGPase" name="KmATPAGPase" value="180"/>
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+ <parameter id="KmADPGAGPase" name="KmADPGAGPase" value="280"/>
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+ <parameter id="KmPPAGPase" name="KmPPAGPase" value="260"/>
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+ <parameter id="KiPAGPase" name="KiPAGPase" value="160"/>
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+ <parameter id="KaPGA3AGPase" name="KaPGA3AGPase" value="10"/>
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+ <parameter id="VmaxStSynth" name="VmaxStSynth" value="171"/>
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+ <parameter id="KmADPGStSynth" name="KmADPGStSynth" value="150"/>
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+ <parameter id="VmaxpPPase" name="VmaxpPPase" value="500"/>
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+ <parameter id="KeqpPPase" name="KeqpPPase" value="750000"/>
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+ <parameter id="VforwardStPase" name="VforwardStPase" value="200"/>
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+ <parameter id="KmPStPase" name="KmPStPase" value="6200"/>
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+ <parameter id="KmG1PStPase" name="KmG1PStPase" value="2600"/>
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+ <parameter id="KeqStPase" name="KeqStPase" value="0.18"/>
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+ <parameter id="Vmaxdegr" name="Vmaxdegr" value="114"/>
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+ <parameter id="KiGlucosedegr" name="KiGlucosedegr" value="100"/>
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+ <parameter id="VGexp" name="VGexp" value="1"/>
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+ <parameter id="kforwardGexp" name="kforwardGexp" value="0.001"/>
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+ <parameter id="kbackwardGexp" name="kbackwardGexp" value="0.001"/>
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+ <parameter id="VG6Pexp" name="VG6Pexp" value="1"/>
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+ <parameter id="kforwardG6Pexp" name="kforwardG6Pexp" value="0.01"/>
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+ <parameter id="kbackwardG6Pexp" name="kbackwardG6Pexp" value="0.01"/>
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+ <parameter id="VmaxpPGM" name="VmaxpPGM" value="1542"/>
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+ <parameter id="KeqpPGM" name="KeqpPGM" value="17"/>
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+ <parameter id="VmaxcPGM" name="VmaxcPGM" value="1842"/>
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+ <parameter id="KeqcPGM" name="KeqcPGM" value="17"/>
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+ <parameter id="VmaxPGI" name="VmaxPGI" value="1086"/>
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+ <parameter id="KmG6PPGI" name="KmG6PPGI" value="270"/>
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+ <parameter id="KmF6PPGI" name="KmF6PPGI" value="150"/>
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+ <parameter id="KeqPGI" name="KeqPGI" value="0.25"/>
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+ <parameter id="KiPEPPGI" name="KiPEPPGI" value="1100"/>
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+ <parameter id="KiF16BPPGI" name="KiF16BPPGI" value="7500"/>
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+ <parameter id="VmaxPFK" name="VmaxPFK" value="135"/>
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+ <parameter id="KmF6PPFK" name="KmF6PPFK" value="290"/>
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+ <parameter id="KiPEPPFK" name="KiPEPPFK" value="18"/>
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+ <parameter id="nPFK" name="nPFK" value="2"/>
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+ <parameter id="LPFK" name="LPFK" value="1"/>
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+ <parameter id="VmaxPFP" name="VmaxPFP" value="1266"/>
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+ <parameter id="KmF6PPFP" name="KmF6PPFP" value="500"/>
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+ <parameter id="KmPPPFP" name="KmPPPFP" value="25"/>
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+ <parameter id="KmF16BPPFP" name="KmF16BPPFP" value="10"/>
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+ <parameter id="KmPPFP" name="KmPPFP" value="10"/>
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+ <parameter id="KeqPFP" name="KeqPFP" value="3.3"/>
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+ <parameter id="Vmaxald" name="Vmaxald" value="430"/>
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+ <parameter id="Keqald" name="Keqald" value="81"/>
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+ <parameter id="KmF16BPald" name="KmF16BPald" value="6"/>
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+ <parameter id="KmGAPald" name="KmGAPald" value="100"/>
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+ <parameter id="KmDHAPald" name="KmDHAPald" value="100"/>
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+ <parameter id="KiGAPald" name="KiGAPald" value="1000"/>
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+ <parameter id="VmaxTPI" name="VmaxTPI" value="4438"/>
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+ <parameter id="KeqTPI" name="KeqTPI" value="0.0455"/>
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+ <parameter id="KmGAPTPI" name="KmGAPTPI" value="440"/>
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+ <parameter id="KmDHAPTPI" name="KmDHAPTPI" value="880"/>
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+ <parameter id="VmaxGAPDH" name="VmaxGAPDH" value="301"/>
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+ <parameter id="KeqGAPDH" name="KeqGAPDH" value="1.724"/>
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+ <parameter id="VPGA3imp" name="VPGA3imp" value="1"/>
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+ <parameter id="kforwardPGA3imp" name="kforwardPGA3imp" value="0.01"/>
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+ <parameter id="kbackwardPGA3imp" name="kbackwardPGA3imp" value="0.01"/>
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+ <parameter id="VmaxPGlyM" name="VmaxPGlyM" value="541"/>
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+ <parameter id="KeqPGlyM" name="KeqPGlyM" value="0.16"/>
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+ <parameter id="KmPGA3PGlyM" name="KmPGA3PGlyM" value="330"/>
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+ <parameter id="KmPGA2PGlyM" name="KmPGA2PGlyM" value="60"/>
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+ <parameter id="Vmaxeno" name="Vmaxeno" value="448"/>
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+ <parameter id="Keqeno" name="Keqeno" value="6.3"/>
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+ <parameter id="KmPGA2eno" name="KmPGA2eno" value="150"/>
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+ <parameter id="KmPEPeno" name="KmPEPeno" value="150"/>
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+ <parameter id="VmaxPK" name="VmaxPK" value="127"/>
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+ <parameter id="KmPEPPK" name="KmPEPPK" value="20"/>
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+ <parameter id="KmADPPK" name="KmADPPK" value="20"/>
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+ <parameter id="KmpyruvatePK" name="KmpyruvatePK" value="1000"/>
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+ <parameter id="KmATPPK" name="KmATPPK" value="86"/>
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+ <parameter id="VforwardUGPase" name="VforwardUGPase" value="8100"/>
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+ <parameter id="KmG1PUGPase" name="KmG1PUGPase" value="80"/>
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+ <parameter id="KmUTPUGPase" name="KmUTPUGPase" value="120"/>
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+ <parameter id="KmUDPGUGPase" name="KmUDPGUGPase" value="140"/>
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+ <parameter id="KmPPUGPase" name="KmPPUGPase" value="130"/>
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+ <parameter id="KeqUGPase" name="KeqUGPase" value="0.15"/>
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+ <parameter id="VmaxSPS" name="VmaxSPS" value="1000"/>
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+ <parameter id="KmF6PSPS" name="KmF6PSPS" value="5000"/>
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+ <parameter id="KmUDPGSPS" name="KmUDPGSPS" value="3000"/>
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+ <parameter id="KiUDPSPS" name="KiUDPSPS" value="1000"/>
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+ <parameter id="KiPSPP" name="KiPSPP" value="4000"/>
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+ <parameter id="VappSPSSPP" name="VappSPSSPP" value="797"/>
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+ <parameter id="KmF6PSPSSPP" name="KmF6PSPSSPP" value="900"/>
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+ <parameter id="KmUDPGSPSSPP" name="KmUDPGSPSSPP" value="2000"/>
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+ <parameter id="KiSucroseSPSSPP" name="KiSucroseSPSSPP" value="5000"/>
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+ <parameter id="KeqSPSSPP" name="KeqSPSSPP" value="7770"/>
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+ <parameter id="VratioSPSSPP" name="VratioSPSSPP" value="1000"/>
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+ <parameter id="VmaxSSynth" name="VmaxSSynth" value="100"/>
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+ <parameter id="KeqSSynth" name="KeqSSynth" value="2.4"/>
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+ <parameter id="KmSSynthFructose" name="KmSSynthFructose" value="5900"/>
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+ <parameter id="KmSSynthUDPG" name="KmSSynthUDPG" value="1650"/>
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+ <parameter id="KmSSynthSucrose" name="KmSSynthSucrose" value="55000"/>
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+ <parameter id="KmSSynthUDP" name="KmSSynthUDP" value="140"/>
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+ <parameter id="KiSSynthGlucose" name="KiSSynthGlucose" value="12000"/>
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+ <parameter id="VSucUpt" name="VSucUpt" value="1"/>
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+ <parameter id="kforwardSucUpt" name="kforwardSucUpt" value="0.01"/>
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+ <parameter id="kbackwardSucUpt" name="kbackwardSucUpt" value="0.01"/>
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+ <parameter id="Vmaxinv" name="Vmaxinv" value="33"/>
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+ <parameter id="KmSucroseinv" name="KmSucroseinv" value="28000"/>
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+ <parameter id="KiFructoseinv" name="KiFructoseinv" value="180"/>
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+ <parameter id="KiGlucoseinv" name="KiGlucoseinv" value="1000"/>
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+ <parameter id="VmaxFK" name="VmaxFK" value="376"/>
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+ <parameter id="KmFructoseFK" name="KmFructoseFK" value="90"/>
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+ <parameter id="KmATPFK" name="KmATPFK" value="35"/>
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+ <parameter id="KiFructoseFK" name="KiFructoseFK" value="5000"/>
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+ <parameter id="KmADPFK" name="KmADPFK" value="13"/>
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+ <parameter id="KmF6PFK" name="KmF6PFK" value="1300"/>
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+ <parameter id="KmGlucoseHK1" name="KmGlucoseHK1" value="41"/>
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+ <parameter id="KmFructoseHK1" name="KmFructoseHK1" value="11000"/>
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+ <parameter id="KmATPHK1" name="KmATPHK1" value="80"/>
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+ <parameter id="KiADPHK1" name="KiADPHK1" value="20"/>
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+ <parameter id="KiG6PHK1" name="KiG6PHK1" value="4100"/>
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+ <parameter id="VmaxHK1" name="VmaxHK1" value="80"/>
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+ <parameter id="VmaxHK2" name="VmaxHK2" value="80"/>
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+ <parameter id="VmaxGK" name="VmaxGK" value="160"/>
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+ <parameter id="KmGlucoseHK2" name="KmGlucoseHK2" value="130"/>
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+ <parameter id="KmFructoseHK2" name="KmFructoseHK2" value="22000"/>
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+ <parameter id="KmATPHK2" name="KmATPHK2" value="280"/>
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+ <parameter id="KiADPHK2" name="KiADPHK2" value="100"/>
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+ <parameter id="VNDPK" name="VNDPK" value="1"/>
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+ <parameter id="kforwardNDPK" name="kforwardNDPK" value="0.001"/>
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+ <parameter id="kbackwardNDPK" name="kbackwardNDPK" value="0.001"/>
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+ <parameter id="VAT" name="VAT" value="1"/>
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+ <parameter id="kforwardAT" name="kforwardAT" value="0.002"/>
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+ <parameter id="kbackwardAT" name="kbackwardAT" value="0.002"/>
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+ <parameter id="VPexp" name="VPexp" value="1"/>
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+ <parameter id="kforwardPexp" name="kforwardPexp" value="0.3"/>
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+ <parameter id="kbackwardPexp" name="kbackwardPexp" value="0.1"/>
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+ <parameter id="VATPcons" name="VATPcons" value="1"/>
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+ <parameter id="kATPcons" name="kATPcons" value="3"/>
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+ </listOfParameters>
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+ <listOfReactions>
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+ <reaction id="vAGPase" name="vAGPase">
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+ <listOfReactants>
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+ <speciesReference species="G1Pam"/>
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+ <speciesReference species="ATPam"/>
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+ </listOfReactants>
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+ <listOfProducts>
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+ <speciesReference species="ADPGam"/>
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+ <speciesReference species="PPam"/>
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+ </listOfProducts>
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+ <listOfModifiers>
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+ <modifierSpeciesReference species="PGA3am"/>
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+ <modifierSpeciesReference species="Pam"/>
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+ </listOfModifiers>
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+ <kineticLaw>
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+ <math xmlns="http://www.w3.org/1998/Math/MathML">
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+ <apply>
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+ <divide/>
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+ <apply>
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+ <divide/>
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+ <apply>
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+ <times/>
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+ <ci> VmaxAGPase </ci>
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+ <apply>
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+ <minus/>
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+ <apply>
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+ <times/>
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+ <ci> G1Pam </ci>
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+ <ci> ATPam </ci>
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+ </apply>
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+ <apply>
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+ <times/>
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+ <ci> ADPGam </ci>
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+ <ci> PPam </ci>
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+ </apply>
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+ </apply>
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+ <apply>
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+ <plus/>
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+ <cn type="integer"> 1 </cn>
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+ <apply>
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+ <divide/>
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+ <ci> PGA3am </ci>
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+ <ci> KaPGA3AGPase </ci>
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+ </apply>
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+ </apply>
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+ </apply>
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+ <apply>
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+ <times/>
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+ <apply>
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+ <plus/>
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+ <apply>
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+ <times/>
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+ <ci> KmG1PAGPase </ci>
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+ <apply>
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+ <plus/>
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+ <cn type="integer"> 1 </cn>
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+ <apply>
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+ <divide/>
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+ <ci> PPam </ci>
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+ <ci> KmPPAGPase </ci>
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+ </apply>
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+ </apply>
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+ </apply>
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+ <ci> G1Pam </ci>
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+ </apply>
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+ <apply>
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+ <plus/>
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+ <apply>
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+ <times/>
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+ <ci> KmATPAGPase </ci>
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+ <apply>
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+ <plus/>
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+ <cn type="integer"> 1 </cn>
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+ <apply>
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+ <divide/>
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+ <ci> ADPGam </ci>
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+ <ci> KmADPGAGPase </ci>
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+ </apply>
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+ </apply>
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+ </apply>
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+ <ci> ATPam </ci>
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+ </apply>
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+ </apply>
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+ </apply>
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+ <apply>
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+ <plus/>
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+ <cn type="integer"> 1 </cn>
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+ <apply>
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+ <divide/>
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+ <ci> Pam </ci>
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+ <ci> KiPAGPase </ci>
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+ </apply>
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+ </apply>
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+ </apply>
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+ </math>
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+ </kineticLaw>
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+ </reaction>
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+ <reaction id="vStSynth" name="vStSynth">
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+ <listOfReactants>
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+ <speciesReference species="ADPGam"/>
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+ <speciesReference species="xstarch"/>
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+ </listOfReactants>
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+ <listOfProducts>
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+ <speciesReference species="ADPam"/>
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+ </listOfProducts>
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+ <kineticLaw>
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+ <math xmlns="http://www.w3.org/1998/Math/MathML">
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+ <apply>
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+ <divide/>
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+ <apply>
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+ <times/>
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+ <ci> VmaxStSynth </ci>
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+ <ci> ADPGam </ci>
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+ </apply>
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+ <apply>
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+ <plus/>
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+ <ci> KmADPGStSynth </ci>
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+ <ci> ADPGam </ci>
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+ </apply>
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+ </apply>
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+ </math>
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+ </kineticLaw>
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+ </reaction>
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+ <reaction id="vpPPase" name="vpPPase">
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+ <listOfReactants>
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+ <speciesReference species="PPam"/>
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+ </listOfReactants>
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+ <listOfProducts>
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+ <speciesReference species="Pam" stoichiometry="2"/>
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+ </listOfProducts>
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+ <kineticLaw>
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+ <math xmlns="http://www.w3.org/1998/Math/MathML">
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+ <apply>
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+ <times/>
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+ <ci> VmaxpPPase </ci>
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+ <apply>
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+ <minus/>
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+ <cn type="integer"> 1 </cn>
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+ <apply>
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+ <divide/>
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+ <apply>
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+ <divide/>
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+ <apply>
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+ <times/>
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+ <ci> Pam </ci>
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+ <ci> Pam </ci>
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+ </apply>
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+ <ci> PPam </ci>
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+ </apply>
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+ <ci> KeqpPPase </ci>
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+ </apply>
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+ </apply>
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+ </apply>
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+ </math>
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+ </kineticLaw>
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+ </reaction>
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+ <reaction id="vStPase" name="vStPase">
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+ <listOfReactants>
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+ <speciesReference species="xstarch"/>
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+ <speciesReference species="Pam"/>
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+ </listOfReactants>
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+ <listOfProducts>
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+ <speciesReference species="G1Pam"/>
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+ </listOfProducts>
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+ <kineticLaw>
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+ <math xmlns="http://www.w3.org/1998/Math/MathML">
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+ <apply>
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+ <divide/>
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+ <apply>
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+ <times/>
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+ <ci> VforwardStPase </ci>
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+ <apply>
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+ <minus/>
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+ <ci> Pam </ci>
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+ <apply>
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+ <divide/>
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+ <ci> G1Pam </ci>
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+ <ci> KeqStPase </ci>
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+ </apply>
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+ </apply>
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+ </apply>
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+ <apply>
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+ <plus/>
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+ <ci> KmPStPase </ci>
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+ <ci> Pam </ci>
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+ <apply>
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+ <divide/>
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+ <apply>
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+ <times/>
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+ <ci> G1Pam </ci>
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+ <ci> KmPStPase </ci>
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+ </apply>
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+ <ci> KmG1PStPase </ci>
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+ </apply>
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+ </apply>
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+ </apply>
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+ </math>
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+ </kineticLaw>
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+ </reaction>
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+ <reaction id="vdegr" name="vdegr">
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+ <listOfReactants>
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+ <speciesReference species="xstarch"/>
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+ </listOfReactants>
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+ <listOfProducts>
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+ <speciesReference species="Glucoseam"/>
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+ </listOfProducts>
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+ <kineticLaw>
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+ <math xmlns="http://www.w3.org/1998/Math/MathML">
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+ <apply>
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+ <divide/>
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+ <ci> Vmaxdegr </ci>
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+ <apply>
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+ <plus/>
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+ <cn type="integer"> 1 </cn>
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+ <apply>
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+ <divide/>
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+ <ci> Glucoseam </ci>
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+ <ci> KiGlucosedegr </ci>
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+ </apply>
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+ </apply>
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+ </apply>
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+ </math>
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+ </kineticLaw>
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+ </reaction>
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+ <reaction id="vGexp" name="vGexp">
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+ <listOfReactants>
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+ <speciesReference species="Glucoseam"/>
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+ </listOfReactants>
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+ <listOfProducts>
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+ <speciesReference species="Glucosecyt"/>
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+ </listOfProducts>
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+ <kineticLaw>
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+ <math xmlns="http://www.w3.org/1998/Math/MathML">
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+ <apply>
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+ <times/>
410
+ <ci> VGexp </ci>
411
+ <apply>
412
+ <minus/>
413
+ <apply>
414
+ <times/>
415
+ <ci> kforwardGexp </ci>
416
+ <ci> Glucoseam </ci>
417
+ </apply>
418
+ <apply>
419
+ <times/>
420
+ <ci> kbackwardGexp </ci>
421
+ <ci> Glucosecyt </ci>
422
+ </apply>
423
+ </apply>
424
+ </apply>
425
+ </math>
426
+ </kineticLaw>
427
+ </reaction>
428
+ <reaction id="vG6Pexp" name="vG6Pexp">
429
+ <listOfReactants>
430
+ <speciesReference species="G6Pam"/>
431
+ <speciesReference species="Pcyt"/>
432
+ </listOfReactants>
433
+ <listOfProducts>
434
+ <speciesReference species="G6Pcyt"/>
435
+ <speciesReference species="Pam"/>
436
+ </listOfProducts>
437
+ <kineticLaw>
438
+ <math xmlns="http://www.w3.org/1998/Math/MathML">
439
+ <apply>
440
+ <times/>
441
+ <ci> VG6Pexp </ci>
442
+ <apply>
443
+ <minus/>
444
+ <apply>
445
+ <times/>
446
+ <ci> kforwardG6Pexp </ci>
447
+ <ci> G6Pam </ci>
448
+ <ci> Pcyt </ci>
449
+ </apply>
450
+ <apply>
451
+ <times/>
452
+ <ci> kbackwardG6Pexp </ci>
453
+ <ci> G6Pcyt </ci>
454
+ <ci> Pam </ci>
455
+ </apply>
456
+ </apply>
457
+ </apply>
458
+ </math>
459
+ </kineticLaw>
460
+ </reaction>
461
+ <reaction id="vpPGM" name="vpPGM">
462
+ <listOfReactants>
463
+ <speciesReference species="G1Pam"/>
464
+ </listOfReactants>
465
+ <listOfProducts>
466
+ <speciesReference species="G6Pam"/>
467
+ </listOfProducts>
468
+ <kineticLaw>
469
+ <math xmlns="http://www.w3.org/1998/Math/MathML">
470
+ <apply>
471
+ <times/>
472
+ <ci> VmaxpPGM </ci>
473
+ <apply>
474
+ <minus/>
475
+ <cn type="integer"> 1 </cn>
476
+ <apply>
477
+ <divide/>
478
+ <apply>
479
+ <divide/>
480
+ <ci> G6Pam </ci>
481
+ <ci> G1Pam </ci>
482
+ </apply>
483
+ <ci> KeqpPGM </ci>
484
+ </apply>
485
+ </apply>
486
+ </apply>
487
+ </math>
488
+ </kineticLaw>
489
+ </reaction>
490
+ <reaction id="vcPGM" name="vcPGM">
491
+ <listOfReactants>
492
+ <speciesReference species="G1Pcyt"/>
493
+ </listOfReactants>
494
+ <listOfProducts>
495
+ <speciesReference species="G6Pcyt"/>
496
+ </listOfProducts>
497
+ <kineticLaw>
498
+ <math xmlns="http://www.w3.org/1998/Math/MathML">
499
+ <apply>
500
+ <times/>
501
+ <ci> VmaxcPGM </ci>
502
+ <apply>
503
+ <minus/>
504
+ <cn type="integer"> 1 </cn>
505
+ <apply>
506
+ <divide/>
507
+ <apply>
508
+ <divide/>
509
+ <ci> G6Pcyt </ci>
510
+ <ci> G1Pcyt </ci>
511
+ </apply>
512
+ <ci> KeqcPGM </ci>
513
+ </apply>
514
+ </apply>
515
+ </apply>
516
+ </math>
517
+ </kineticLaw>
518
+ </reaction>
519
+ <reaction id="vPGI" name="vPGI">
520
+ <listOfReactants>
521
+ <speciesReference species="G6Pcyt"/>
522
+ </listOfReactants>
523
+ <listOfProducts>
524
+ <speciesReference species="F6Pcyt"/>
525
+ </listOfProducts>
526
+ <listOfModifiers>
527
+ <modifierSpeciesReference species="F16BPcyt"/>
528
+ <modifierSpeciesReference species="PEPcyt"/>
529
+ </listOfModifiers>
530
+ <kineticLaw>
531
+ <math xmlns="http://www.w3.org/1998/Math/MathML">
532
+ <apply>
533
+ <divide/>
534
+ <apply>
535
+ <times/>
536
+ <ci> VmaxPGI </ci>
537
+ <apply>
538
+ <minus/>
539
+ <ci> G6Pcyt </ci>
540
+ <apply>
541
+ <divide/>
542
+ <ci> F6Pcyt </ci>
543
+ <ci> KeqPGI </ci>
544
+ </apply>
545
+ </apply>
546
+ </apply>
547
+ <apply>
548
+ <plus/>
549
+ <ci> KmG6PPGI </ci>
550
+ <ci> G6Pcyt </ci>
551
+ <apply>
552
+ <divide/>
553
+ <apply>
554
+ <times/>
555
+ <ci> F6Pcyt </ci>
556
+ <ci> KmG6PPGI </ci>
557
+ </apply>
558
+ <ci> KmF6PPGI </ci>
559
+ </apply>
560
+ <apply>
561
+ <divide/>
562
+ <apply>
563
+ <times/>
564
+ <ci> F16BPcyt </ci>
565
+ <ci> KmG6PPGI </ci>
566
+ </apply>
567
+ <ci> KiF16BPPGI </ci>
568
+ </apply>
569
+ <apply>
570
+ <divide/>
571
+ <apply>
572
+ <times/>
573
+ <ci> PEPcyt </ci>
574
+ <ci> KmG6PPGI </ci>
575
+ </apply>
576
+ <ci> KiPEPPGI </ci>
577
+ </apply>
578
+ </apply>
579
+ </apply>
580
+ </math>
581
+ </kineticLaw>
582
+ </reaction>
583
+ <reaction id="vPFK" name="vPFK">
584
+ <listOfReactants>
585
+ <speciesReference species="F6Pcyt"/>
586
+ <speciesReference species="ATPcyt"/>
587
+ </listOfReactants>
588
+ <listOfProducts>
589
+ <speciesReference species="F16BPcyt"/>
590
+ <speciesReference species="ADPcyt"/>
591
+ </listOfProducts>
592
+ <listOfModifiers>
593
+ <modifierSpeciesReference species="PEPcyt"/>
594
+ </listOfModifiers>
595
+ <kineticLaw>
596
+ <math xmlns="http://www.w3.org/1998/Math/MathML">
597
+ <apply>
598
+ <divide/>
599
+ <apply>
600
+ <times/>
601
+ <ci> VmaxPFK </ci>
602
+ <apply>
603
+ <divide/>
604
+ <ci> F6Pcyt </ci>
605
+ <ci> KmF6PPFK </ci>
606
+ </apply>
607
+ <apply>
608
+ <power/>
609
+ <apply>
610
+ <plus/>
611
+ <cn type="integer"> 1 </cn>
612
+ <apply>
613
+ <divide/>
614
+ <ci> F6Pcyt </ci>
615
+ <ci> KmF6PPFK </ci>
616
+ </apply>
617
+ </apply>
618
+ <apply>
619
+ <minus/>
620
+ <ci> nPFK </ci>
621
+ <cn type="integer"> 1 </cn>
622
+ </apply>
623
+ </apply>
624
+ </apply>
625
+ <apply>
626
+ <plus/>
627
+ <apply>
628
+ <power/>
629
+ <apply>
630
+ <plus/>
631
+ <cn type="integer"> 1 </cn>
632
+ <apply>
633
+ <divide/>
634
+ <ci> F6Pcyt </ci>
635
+ <ci> KmF6PPFK </ci>
636
+ </apply>
637
+ </apply>
638
+ <ci> nPFK </ci>
639
+ </apply>
640
+ <apply>
641
+ <times/>
642
+ <ci> LPFK </ci>
643
+ <apply>
644
+ <power/>
645
+ <apply>
646
+ <plus/>
647
+ <cn type="integer"> 1 </cn>
648
+ <apply>
649
+ <divide/>
650
+ <ci> PEPcyt </ci>
651
+ <ci> KiPEPPFK </ci>
652
+ </apply>
653
+ </apply>
654
+ <ci> nPFK </ci>
655
+ </apply>
656
+ </apply>
657
+ </apply>
658
+ </apply>
659
+ </math>
660
+ </kineticLaw>
661
+ </reaction>
662
+ <reaction id="vPFP" name="vPFP">
663
+ <listOfReactants>
664
+ <speciesReference species="F6Pcyt"/>
665
+ <speciesReference species="PPcyt"/>
666
+ </listOfReactants>
667
+ <listOfProducts>
668
+ <speciesReference species="F16BPcyt"/>
669
+ <speciesReference species="Pcyt"/>
670
+ </listOfProducts>
671
+ <kineticLaw>
672
+ <math xmlns="http://www.w3.org/1998/Math/MathML">
673
+ <apply>
674
+ <divide/>
675
+ <apply>
676
+ <times/>
677
+ <ci> VmaxPFP </ci>
678
+ <apply>
679
+ <divide/>
680
+ <apply>
681
+ <divide/>
682
+ <cn type="integer"> 1 </cn>
683
+ <ci> KmF6PPFP </ci>
684
+ </apply>
685
+ <ci> KmPPPFP </ci>
686
+ </apply>
687
+ <apply>
688
+ <minus/>
689
+ <apply>
690
+ <times/>
691
+ <ci> F6Pcyt </ci>
692
+ <ci> PPcyt </ci>
693
+ </apply>
694
+ <apply>
695
+ <divide/>
696
+ <apply>
697
+ <times/>
698
+ <ci> F16BPcyt </ci>
699
+ <ci> Pcyt </ci>
700
+ </apply>
701
+ <ci> KeqPFP </ci>
702
+ </apply>
703
+ </apply>
704
+ </apply>
705
+ <apply>
706
+ <plus/>
707
+ <cn type="integer"> 1 </cn>
708
+ <apply>
709
+ <divide/>
710
+ <ci> F6Pcyt </ci>
711
+ <ci> KmF6PPFP </ci>
712
+ </apply>
713
+ <apply>
714
+ <divide/>
715
+ <ci> PPcyt </ci>
716
+ <ci> KmPPPFP </ci>
717
+ </apply>
718
+ <apply>
719
+ <divide/>
720
+ <ci> F16BPcyt </ci>
721
+ <ci> KmF16BPPFP </ci>
722
+ </apply>
723
+ <apply>
724
+ <divide/>
725
+ <ci> Pcyt </ci>
726
+ <ci> KmPPFP </ci>
727
+ </apply>
728
+ </apply>
729
+ </apply>
730
+ </math>
731
+ </kineticLaw>
732
+ </reaction>
733
+ <reaction id="vald" name="vald">
734
+ <listOfReactants>
735
+ <speciesReference species="F16BPcyt"/>
736
+ </listOfReactants>
737
+ <listOfProducts>
738
+ <speciesReference species="GAPcyt"/>
739
+ <speciesReference species="DHAPcyt"/>
740
+ </listOfProducts>
741
+ <kineticLaw>
742
+ <math xmlns="http://www.w3.org/1998/Math/MathML">
743
+ <apply>
744
+ <divide/>
745
+ <apply>
746
+ <times/>
747
+ <ci> Vmaxald </ci>
748
+ <apply>
749
+ <divide/>
750
+ <ci> F16BPcyt </ci>
751
+ <ci> KmF16BPald </ci>
752
+ </apply>
753
+ <apply>
754
+ <minus/>
755
+ <cn type="integer"> 1 </cn>
756
+ <apply>
757
+ <divide/>
758
+ <apply>
759
+ <divide/>
760
+ <apply>
761
+ <times/>
762
+ <ci> GAPcyt </ci>
763
+ <ci> DHAPcyt </ci>
764
+ </apply>
765
+ <ci> F16BPcyt </ci>
766
+ </apply>
767
+ <ci> Keqald </ci>
768
+ </apply>
769
+ </apply>
770
+ </apply>
771
+ <apply>
772
+ <plus/>
773
+ <cn type="integer"> 1 </cn>
774
+ <apply>
775
+ <divide/>
776
+ <ci> F16BPcyt </ci>
777
+ <ci> KmF16BPald </ci>
778
+ </apply>
779
+ <apply>
780
+ <divide/>
781
+ <ci> GAPcyt </ci>
782
+ <ci> KmGAPald </ci>
783
+ </apply>
784
+ <apply>
785
+ <divide/>
786
+ <ci> DHAPcyt </ci>
787
+ <ci> KmDHAPald </ci>
788
+ </apply>
789
+ <apply>
790
+ <divide/>
791
+ <apply>
792
+ <times/>
793
+ <ci> F16BPcyt </ci>
794
+ <ci> GAPcyt </ci>
795
+ </apply>
796
+ <apply>
797
+ <times/>
798
+ <ci> KmF16BPald </ci>
799
+ <ci> KiGAPald </ci>
800
+ </apply>
801
+ </apply>
802
+ <apply>
803
+ <divide/>
804
+ <apply>
805
+ <times/>
806
+ <ci> GAPcyt </ci>
807
+ <ci> DHAPcyt </ci>
808
+ </apply>
809
+ <apply>
810
+ <times/>
811
+ <ci> KmGAPald </ci>
812
+ <ci> KmDHAPald </ci>
813
+ </apply>
814
+ </apply>
815
+ </apply>
816
+ </apply>
817
+ </math>
818
+ </kineticLaw>
819
+ </reaction>
820
+ <reaction id="vTPI" name="vTPI">
821
+ <listOfReactants>
822
+ <speciesReference species="DHAPcyt"/>
823
+ </listOfReactants>
824
+ <listOfProducts>
825
+ <speciesReference species="GAPcyt"/>
826
+ </listOfProducts>
827
+ <kineticLaw>
828
+ <math xmlns="http://www.w3.org/1998/Math/MathML">
829
+ <apply>
830
+ <divide/>
831
+ <apply>
832
+ <times/>
833
+ <ci> VmaxTPI </ci>
834
+ <apply>
835
+ <minus/>
836
+ <ci> DHAPcyt </ci>
837
+ <apply>
838
+ <divide/>
839
+ <ci> GAPcyt </ci>
840
+ <ci> KeqTPI </ci>
841
+ </apply>
842
+ </apply>
843
+ </apply>
844
+ <apply>
845
+ <plus/>
846
+ <ci> KmDHAPTPI </ci>
847
+ <ci> DHAPcyt </ci>
848
+ <apply>
849
+ <divide/>
850
+ <apply>
851
+ <times/>
852
+ <ci> GAPcyt </ci>
853
+ <ci> KmGAPTPI </ci>
854
+ </apply>
855
+ <ci> KmGAPTPI </ci>
856
+ </apply>
857
+ </apply>
858
+ </apply>
859
+ </math>
860
+ </kineticLaw>
861
+ </reaction>
862
+ <reaction id="vGAPDH" name="vGAPDH">
863
+ <listOfReactants>
864
+ <speciesReference species="GAPcyt" stoichiometry="6"/>
865
+ <speciesReference species="ADPcyt" stoichiometry="17"/>
866
+ <speciesReference species="Pcyt" stoichiometry="17"/>
867
+ </listOfReactants>
868
+ <listOfProducts>
869
+ <speciesReference species="PGA3cyt" stoichiometry="6"/>
870
+ <speciesReference species="ATPcyt" stoichiometry="17"/>
871
+ </listOfProducts>
872
+ <kineticLaw>
873
+ <math xmlns="http://www.w3.org/1998/Math/MathML">
874
+ <apply>
875
+ <times/>
876
+ <apply>
877
+ <divide/>
878
+ <ci> VmaxGAPDH </ci>
879
+ <cn type="integer"> 6 </cn>
880
+ </apply>
881
+ <apply>
882
+ <minus/>
883
+ <cn type="integer"> 1 </cn>
884
+ <apply>
885
+ <divide/>
886
+ <apply>
887
+ <divide/>
888
+ <apply>
889
+ <times/>
890
+ <ci> PGA3cyt </ci>
891
+ <ci> ATPcyt </ci>
892
+ </apply>
893
+ <apply>
894
+ <times/>
895
+ <ci> GAPcyt </ci>
896
+ <ci> Pcyt </ci>
897
+ <ci> ADPcyt </ci>
898
+ </apply>
899
+ </apply>
900
+ <ci> KeqGAPDH </ci>
901
+ </apply>
902
+ </apply>
903
+ </apply>
904
+ </math>
905
+ </kineticLaw>
906
+ </reaction>
907
+ <reaction id="vPGA3imp" name="vPGA3imp">
908
+ <listOfReactants>
909
+ <speciesReference species="PGA3cyt"/>
910
+ <speciesReference species="G6Pam"/>
911
+ </listOfReactants>
912
+ <listOfProducts>
913
+ <speciesReference species="PGA3am"/>
914
+ <speciesReference species="G6Pcyt"/>
915
+ </listOfProducts>
916
+ <kineticLaw>
917
+ <math xmlns="http://www.w3.org/1998/Math/MathML">
918
+ <apply>
919
+ <times/>
920
+ <ci> VPGA3imp </ci>
921
+ <apply>
922
+ <minus/>
923
+ <apply>
924
+ <times/>
925
+ <ci> kforwardPGA3imp </ci>
926
+ <ci> PGA3cyt </ci>
927
+ <ci> G6Pam </ci>
928
+ </apply>
929
+ <apply>
930
+ <times/>
931
+ <ci> kbackwardPGA3imp </ci>
932
+ <ci> PGA3am </ci>
933
+ <ci> G6Pcyt </ci>
934
+ </apply>
935
+ </apply>
936
+ </apply>
937
+ </math>
938
+ </kineticLaw>
939
+ </reaction>
940
+ <reaction id="vPGlyM" name="vPGlyM">
941
+ <listOfReactants>
942
+ <speciesReference species="PGA3cyt"/>
943
+ </listOfReactants>
944
+ <listOfProducts>
945
+ <speciesReference species="PGA2cyt"/>
946
+ </listOfProducts>
947
+ <kineticLaw>
948
+ <math xmlns="http://www.w3.org/1998/Math/MathML">
949
+ <apply>
950
+ <divide/>
951
+ <apply>
952
+ <times/>
953
+ <ci> VmaxPGlyM </ci>
954
+ <apply>
955
+ <minus/>
956
+ <ci> PGA3cyt </ci>
957
+ <apply>
958
+ <divide/>
959
+ <ci> PGA2cyt </ci>
960
+ <ci> KeqPGlyM </ci>
961
+ </apply>
962
+ </apply>
963
+ </apply>
964
+ <apply>
965
+ <plus/>
966
+ <ci> KmPGA3PGlyM </ci>
967
+ <ci> PGA3cyt </ci>
968
+ <apply>
969
+ <divide/>
970
+ <apply>
971
+ <times/>
972
+ <ci> PGA2cyt </ci>
973
+ <ci> KmPGA3PGlyM </ci>
974
+ </apply>
975
+ <ci> KmPGA2PGlyM </ci>
976
+ </apply>
977
+ </apply>
978
+ </apply>
979
+ </math>
980
+ </kineticLaw>
981
+ </reaction>
982
+ <reaction id="veno" name="veno">
983
+ <listOfReactants>
984
+ <speciesReference species="PGA2cyt"/>
985
+ </listOfReactants>
986
+ <listOfProducts>
987
+ <speciesReference species="PEPcyt"/>
988
+ </listOfProducts>
989
+ <kineticLaw>
990
+ <math xmlns="http://www.w3.org/1998/Math/MathML">
991
+ <apply>
992
+ <divide/>
993
+ <apply>
994
+ <times/>
995
+ <ci> Vmaxeno </ci>
996
+ <apply>
997
+ <minus/>
998
+ <ci> PGA2cyt </ci>
999
+ <apply>
1000
+ <divide/>
1001
+ <ci> PEPcyt </ci>
1002
+ <ci> Keqeno </ci>
1003
+ </apply>
1004
+ </apply>
1005
+ </apply>
1006
+ <apply>
1007
+ <plus/>
1008
+ <ci> KmPGA2eno </ci>
1009
+ <ci> PGA2cyt </ci>
1010
+ <apply>
1011
+ <divide/>
1012
+ <apply>
1013
+ <times/>
1014
+ <ci> PEPcyt </ci>
1015
+ <ci> KmPGA2eno </ci>
1016
+ </apply>
1017
+ <ci> KmPEPeno </ci>
1018
+ </apply>
1019
+ </apply>
1020
+ </apply>
1021
+ </math>
1022
+ </kineticLaw>
1023
+ </reaction>
1024
+ <reaction id="vPK" name="vPK">
1025
+ <listOfReactants>
1026
+ <speciesReference species="PEPcyt"/>
1027
+ <speciesReference species="ADPcyt"/>
1028
+ </listOfReactants>
1029
+ <listOfProducts>
1030
+ <speciesReference species="xpyruvate"/>
1031
+ <speciesReference species="ATPcyt"/>
1032
+ </listOfProducts>
1033
+ <kineticLaw>
1034
+ <math xmlns="http://www.w3.org/1998/Math/MathML">
1035
+ <apply>
1036
+ <divide/>
1037
+ <apply>
1038
+ <divide/>
1039
+ <apply>
1040
+ <times/>
1041
+ <ci> VmaxPK </ci>
1042
+ <ci> PEPcyt </ci>
1043
+ <ci> ADPcyt </ci>
1044
+ </apply>
1045
+ <apply>
1046
+ <times/>
1047
+ <ci> KmPEPPK </ci>
1048
+ <ci> KmADPPK </ci>
1049
+ </apply>
1050
+ </apply>
1051
+ <apply>
1052
+ <plus/>
1053
+ <cn type="integer"> 1 </cn>
1054
+ <apply>
1055
+ <divide/>
1056
+ <ci> PEPcyt </ci>
1057
+ <ci> KmPEPPK </ci>
1058
+ </apply>
1059
+ <apply>
1060
+ <divide/>
1061
+ <apply>
1062
+ <times/>
1063
+ <ci> PEPcyt </ci>
1064
+ <ci> ADPcyt </ci>
1065
+ </apply>
1066
+ <apply>
1067
+ <times/>
1068
+ <ci> KmPEPPK </ci>
1069
+ <ci> KmADPPK </ci>
1070
+ </apply>
1071
+ </apply>
1072
+ <apply>
1073
+ <divide/>
1074
+ <ci> ATPcyt </ci>
1075
+ <ci> KmATPPK </ci>
1076
+ </apply>
1077
+ <apply>
1078
+ <divide/>
1079
+ <apply>
1080
+ <times/>
1081
+ <ci> xpyruvate </ci>
1082
+ <ci> ATPcyt </ci>
1083
+ </apply>
1084
+ <apply>
1085
+ <times/>
1086
+ <ci> KmpyruvatePK </ci>
1087
+ <ci> KmATPPK </ci>
1088
+ </apply>
1089
+ </apply>
1090
+ </apply>
1091
+ </apply>
1092
+ </math>
1093
+ </kineticLaw>
1094
+ </reaction>
1095
+ <reaction id="vUGPase" name="vUGPase">
1096
+ <listOfReactants>
1097
+ <speciesReference species="G1Pcyt"/>
1098
+ <speciesReference species="UTPcyt"/>
1099
+ </listOfReactants>
1100
+ <listOfProducts>
1101
+ <speciesReference species="UDPGcyt"/>
1102
+ <speciesReference species="PPcyt"/>
1103
+ </listOfProducts>
1104
+ <kineticLaw>
1105
+ <math xmlns="http://www.w3.org/1998/Math/MathML">
1106
+ <apply>
1107
+ <divide/>
1108
+ <apply>
1109
+ <times/>
1110
+ <ci> VforwardUGPase </ci>
1111
+ <apply>
1112
+ <minus/>
1113
+ <apply>
1114
+ <times/>
1115
+ <ci> G1Pcyt </ci>
1116
+ <ci> UTPcyt </ci>
1117
+ </apply>
1118
+ <apply>
1119
+ <divide/>
1120
+ <apply>
1121
+ <times/>
1122
+ <ci> UDPGcyt </ci>
1123
+ <ci> PPcyt </ci>
1124
+ </apply>
1125
+ <ci> KeqUGPase </ci>
1126
+ </apply>
1127
+ </apply>
1128
+ </apply>
1129
+ <apply>
1130
+ <times/>
1131
+ <apply>
1132
+ <plus/>
1133
+ <apply>
1134
+ <times/>
1135
+ <ci> KmG1PUGPase </ci>
1136
+ <apply>
1137
+ <plus/>
1138
+ <cn type="integer"> 1 </cn>
1139
+ <apply>
1140
+ <divide/>
1141
+ <ci> PPcyt </ci>
1142
+ <ci> KmPPUGPase </ci>
1143
+ </apply>
1144
+ </apply>
1145
+ </apply>
1146
+ <ci> G1Pcyt </ci>
1147
+ </apply>
1148
+ <apply>
1149
+ <plus/>
1150
+ <apply>
1151
+ <times/>
1152
+ <ci> KmUTPUGPase </ci>
1153
+ <apply>
1154
+ <plus/>
1155
+ <cn type="integer"> 1 </cn>
1156
+ <apply>
1157
+ <divide/>
1158
+ <ci> UDPGcyt </ci>
1159
+ <ci> KmUDPGUGPase </ci>
1160
+ </apply>
1161
+ </apply>
1162
+ </apply>
1163
+ <ci> UTPcyt </ci>
1164
+ </apply>
1165
+ </apply>
1166
+ </apply>
1167
+ </math>
1168
+ </kineticLaw>
1169
+ </reaction>
1170
+ <reaction id="vSPSSPP" name="vSPSSPP">
1171
+ <listOfReactants>
1172
+ <speciesReference species="F6Pcyt"/>
1173
+ <speciesReference species="UDPGcyt"/>
1174
+ </listOfReactants>
1175
+ <listOfProducts>
1176
+ <speciesReference species="Sucrose"/>
1177
+ <speciesReference species="Pcyt"/>
1178
+ <speciesReference species="UDPcyt"/>
1179
+ </listOfProducts>
1180
+ <kineticLaw>
1181
+ <math xmlns="http://www.w3.org/1998/Math/MathML">
1182
+ <apply>
1183
+ <divide/>
1184
+ <apply>
1185
+ <times/>
1186
+ <ci> VappSPSSPP </ci>
1187
+ <apply>
1188
+ <minus/>
1189
+ <apply>
1190
+ <times/>
1191
+ <ci> F6Pcyt </ci>
1192
+ <ci> UDPGcyt </ci>
1193
+ </apply>
1194
+ <apply>
1195
+ <divide/>
1196
+ <apply>
1197
+ <times/>
1198
+ <ci> UDPcyt </ci>
1199
+ <ci> Pcyt </ci>
1200
+ </apply>
1201
+ <ci> KeqSPSSPP </ci>
1202
+ </apply>
1203
+ </apply>
1204
+ </apply>
1205
+ <apply>
1206
+ <plus/>
1207
+ <apply>
1208
+ <times/>
1209
+ <ci> KmF6PSPSSPP </ci>
1210
+ <ci> KmUDPGSPSSPP </ci>
1211
+ </apply>
1212
+ <apply>
1213
+ <times/>
1214
+ <ci> F6Pcyt </ci>
1215
+ <ci> UDPGcyt </ci>
1216
+ </apply>
1217
+ <apply>
1218
+ <divide/>
1219
+ <apply>
1220
+ <times/>
1221
+ <ci> UDPcyt </ci>
1222
+ <ci> Pcyt </ci>
1223
+ <ci> VratioSPSSPP </ci>
1224
+ </apply>
1225
+ <ci> KeqSPSSPP </ci>
1226
+ </apply>
1227
+ <apply>
1228
+ <divide/>
1229
+ <apply>
1230
+ <times/>
1231
+ <ci> Sucrose </ci>
1232
+ <ci> KmF6PSPSSPP </ci>
1233
+ <ci> KmUDPGSPSSPP </ci>
1234
+ </apply>
1235
+ <ci> KiSucroseSPSSPP </ci>
1236
+ </apply>
1237
+ </apply>
1238
+ </apply>
1239
+ </math>
1240
+ </kineticLaw>
1241
+ </reaction>
1242
+ <reaction id="vSSynth" name="vSSynth">
1243
+ <listOfReactants>
1244
+ <speciesReference species="Fructose"/>
1245
+ <speciesReference species="UDPGcyt"/>
1246
+ </listOfReactants>
1247
+ <listOfProducts>
1248
+ <speciesReference species="Sucrose"/>
1249
+ <speciesReference species="UDPcyt"/>
1250
+ </listOfProducts>
1251
+ <listOfModifiers>
1252
+ <modifierSpeciesReference species="Glucosecyt"/>
1253
+ </listOfModifiers>
1254
+ <kineticLaw>
1255
+ <math xmlns="http://www.w3.org/1998/Math/MathML">
1256
+ <apply>
1257
+ <divide/>
1258
+ <apply>
1259
+ <divide/>
1260
+ <apply>
1261
+ <times/>
1262
+ <ci> VmaxSSynth </ci>
1263
+ <apply>
1264
+ <divide/>
1265
+ <apply>
1266
+ <times/>
1267
+ <ci> Fructose </ci>
1268
+ <ci> UDPGcyt </ci>
1269
+ </apply>
1270
+ <apply>
1271
+ <times/>
1272
+ <ci> KmSSynthFructose </ci>
1273
+ <ci> KmSSynthUDPG </ci>
1274
+ </apply>
1275
+ </apply>
1276
+ <apply>
1277
+ <minus/>
1278
+ <cn type="integer"> 1 </cn>
1279
+ <apply>
1280
+ <divide/>
1281
+ <apply>
1282
+ <divide/>
1283
+ <apply>
1284
+ <divide/>
1285
+ <apply>
1286
+ <times/>
1287
+ <ci> Sucrose </ci>
1288
+ <ci> UDPcyt </ci>
1289
+ </apply>
1290
+ <ci> Fructose </ci>
1291
+ </apply>
1292
+ <ci> UDPGcyt </ci>
1293
+ </apply>
1294
+ <ci> KeqSSynth </ci>
1295
+ </apply>
1296
+ </apply>
1297
+ </apply>
1298
+ <apply>
1299
+ <plus/>
1300
+ <cn type="integer"> 1 </cn>
1301
+ <apply>
1302
+ <divide/>
1303
+ <apply>
1304
+ <times/>
1305
+ <ci> Fructose </ci>
1306
+ <ci> UDPGcyt </ci>
1307
+ </apply>
1308
+ <apply>
1309
+ <times/>
1310
+ <ci> KmSSynthFructose </ci>
1311
+ <ci> KmSSynthUDPG </ci>
1312
+ </apply>
1313
+ </apply>
1314
+ <apply>
1315
+ <divide/>
1316
+ <apply>
1317
+ <times/>
1318
+ <ci> Sucrose </ci>
1319
+ <ci> UDPcyt </ci>
1320
+ </apply>
1321
+ <apply>
1322
+ <times/>
1323
+ <ci> KmSSynthSucrose </ci>
1324
+ <ci> KmSSynthUDP </ci>
1325
+ </apply>
1326
+ </apply>
1327
+ </apply>
1328
+ </apply>
1329
+ <apply>
1330
+ <plus/>
1331
+ <cn type="integer"> 1 </cn>
1332
+ <apply>
1333
+ <divide/>
1334
+ <ci> Glucosecyt </ci>
1335
+ <ci> KiSSynthGlucose </ci>
1336
+ </apply>
1337
+ </apply>
1338
+ </apply>
1339
+ </math>
1340
+ </kineticLaw>
1341
+ </reaction>
1342
+ <reaction id="vSucUpt" name="vSucUpt">
1343
+ <listOfReactants>
1344
+ <speciesReference species="xsucrose"/>
1345
+ </listOfReactants>
1346
+ <listOfProducts>
1347
+ <speciesReference species="Sucrose"/>
1348
+ </listOfProducts>
1349
+ <kineticLaw>
1350
+ <math xmlns="http://www.w3.org/1998/Math/MathML">
1351
+ <apply>
1352
+ <times/>
1353
+ <ci> VSucUpt </ci>
1354
+ <apply>
1355
+ <minus/>
1356
+ <apply>
1357
+ <times/>
1358
+ <ci> kforwardSucUpt </ci>
1359
+ <ci> xsucrose </ci>
1360
+ </apply>
1361
+ <apply>
1362
+ <times/>
1363
+ <ci> kbackwardSucUpt </ci>
1364
+ <ci> Sucrose </ci>
1365
+ </apply>
1366
+ </apply>
1367
+ </apply>
1368
+ </math>
1369
+ </kineticLaw>
1370
+ </reaction>
1371
+ <reaction id="vinv" name="vinv">
1372
+ <listOfReactants>
1373
+ <speciesReference species="Sucrose"/>
1374
+ </listOfReactants>
1375
+ <listOfProducts>
1376
+ <speciesReference species="Fructose"/>
1377
+ <speciesReference species="Glucosecyt"/>
1378
+ </listOfProducts>
1379
+ <kineticLaw>
1380
+ <math xmlns="http://www.w3.org/1998/Math/MathML">
1381
+ <apply>
1382
+ <divide/>
1383
+ <apply>
1384
+ <times/>
1385
+ <ci> Vmaxinv </ci>
1386
+ <apply>
1387
+ <divide/>
1388
+ <ci> Sucrose </ci>
1389
+ <ci> KmSucroseinv </ci>
1390
+ </apply>
1391
+ </apply>
1392
+ <apply>
1393
+ <times/>
1394
+ <apply>
1395
+ <plus/>
1396
+ <cn type="integer"> 1 </cn>
1397
+ <apply>
1398
+ <divide/>
1399
+ <ci> Sucrose </ci>
1400
+ <ci> KmSucroseinv </ci>
1401
+ </apply>
1402
+ <apply>
1403
+ <divide/>
1404
+ <ci> Fructose </ci>
1405
+ <ci> KiFructoseinv </ci>
1406
+ </apply>
1407
+ </apply>
1408
+ <apply>
1409
+ <plus/>
1410
+ <cn type="integer"> 1 </cn>
1411
+ <apply>
1412
+ <divide/>
1413
+ <ci> Glucosecyt </ci>
1414
+ <ci> KiGlucoseinv </ci>
1415
+ </apply>
1416
+ </apply>
1417
+ </apply>
1418
+ </apply>
1419
+ </math>
1420
+ </kineticLaw>
1421
+ </reaction>
1422
+ <reaction id="vFK" name="vFK">
1423
+ <listOfReactants>
1424
+ <speciesReference species="Fructose"/>
1425
+ <speciesReference species="ATPcyt"/>
1426
+ </listOfReactants>
1427
+ <listOfProducts>
1428
+ <speciesReference species="F6Pcyt"/>
1429
+ <speciesReference species="ADPcyt"/>
1430
+ </listOfProducts>
1431
+ <kineticLaw>
1432
+ <math xmlns="http://www.w3.org/1998/Math/MathML">
1433
+ <apply>
1434
+ <divide/>
1435
+ <apply>
1436
+ <times/>
1437
+ <ci> VmaxFK </ci>
1438
+ <apply>
1439
+ <divide/>
1440
+ <apply>
1441
+ <times/>
1442
+ <ci> Fructose </ci>
1443
+ <ci> ATPcyt </ci>
1444
+ </apply>
1445
+ <apply>
1446
+ <times/>
1447
+ <ci> KmFructoseFK </ci>
1448
+ <ci> KmATPFK </ci>
1449
+ </apply>
1450
+ </apply>
1451
+ </apply>
1452
+ <apply>
1453
+ <times/>
1454
+ <apply>
1455
+ <plus/>
1456
+ <cn type="integer"> 1 </cn>
1457
+ <apply>
1458
+ <divide/>
1459
+ <ci> Fructose </ci>
1460
+ <ci> KmFructoseFK </ci>
1461
+ </apply>
1462
+ </apply>
1463
+ <apply>
1464
+ <plus/>
1465
+ <cn type="integer"> 1 </cn>
1466
+ <apply>
1467
+ <divide/>
1468
+ <ci> Fructose </ci>
1469
+ <ci> KiFructoseFK </ci>
1470
+ </apply>
1471
+ </apply>
1472
+ <apply>
1473
+ <plus/>
1474
+ <cn type="integer"> 1 </cn>
1475
+ <apply>
1476
+ <divide/>
1477
+ <ci> F6Pcyt </ci>
1478
+ <ci> KmF6PFK </ci>
1479
+ </apply>
1480
+ </apply>
1481
+ <apply>
1482
+ <plus/>
1483
+ <cn type="integer"> 1 </cn>
1484
+ <apply>
1485
+ <divide/>
1486
+ <ci> ATPcyt </ci>
1487
+ <ci> KmATPFK </ci>
1488
+ </apply>
1489
+ <apply>
1490
+ <divide/>
1491
+ <ci> Fructose </ci>
1492
+ <ci> KiFructoseFK </ci>
1493
+ </apply>
1494
+ <apply>
1495
+ <divide/>
1496
+ <ci> ADPcyt </ci>
1497
+ <ci> KmADPFK </ci>
1498
+ </apply>
1499
+ </apply>
1500
+ </apply>
1501
+ </apply>
1502
+ </math>
1503
+ </kineticLaw>
1504
+ </reaction>
1505
+ <reaction id="vHK" name="vHK">
1506
+ <listOfReactants>
1507
+ <speciesReference species="Glucosecyt"/>
1508
+ <speciesReference species="ATPcyt"/>
1509
+ </listOfReactants>
1510
+ <listOfProducts>
1511
+ <speciesReference species="G6Pcyt"/>
1512
+ <speciesReference species="ADPcyt"/>
1513
+ </listOfProducts>
1514
+ <listOfModifiers>
1515
+ <modifierSpeciesReference species="Fructose"/>
1516
+ <modifierSpeciesReference species="Fructose"/>
1517
+ </listOfModifiers>
1518
+ <kineticLaw>
1519
+ <math xmlns="http://www.w3.org/1998/Math/MathML">
1520
+ <apply>
1521
+ <plus/>
1522
+ <apply>
1523
+ <divide/>
1524
+ <apply>
1525
+ <times/>
1526
+ <apply>
1527
+ <divide/>
1528
+ <ci> VmaxGK </ci>
1529
+ <cn type="integer"> 2 </cn>
1530
+ </apply>
1531
+ <apply>
1532
+ <divide/>
1533
+ <apply>
1534
+ <times/>
1535
+ <ci> Glucosecyt </ci>
1536
+ <ci> ATPcyt </ci>
1537
+ </apply>
1538
+ <apply>
1539
+ <times/>
1540
+ <ci> KmGlucoseHK1 </ci>
1541
+ <ci> KmATPHK1 </ci>
1542
+ </apply>
1543
+ </apply>
1544
+ </apply>
1545
+ <apply>
1546
+ <times/>
1547
+ <apply>
1548
+ <plus/>
1549
+ <cn type="integer"> 1 </cn>
1550
+ <apply>
1551
+ <divide/>
1552
+ <ci> Glucosecyt </ci>
1553
+ <ci> KmGlucoseHK1 </ci>
1554
+ </apply>
1555
+ <apply>
1556
+ <divide/>
1557
+ <ci> Fructose </ci>
1558
+ <ci> KmFructoseHK1 </ci>
1559
+ </apply>
1560
+ </apply>
1561
+ <apply>
1562
+ <plus/>
1563
+ <cn type="integer"> 1 </cn>
1564
+ <apply>
1565
+ <divide/>
1566
+ <ci> ATPcyt </ci>
1567
+ <ci> KmATPHK1 </ci>
1568
+ </apply>
1569
+ <apply>
1570
+ <divide/>
1571
+ <ci> ADPcyt </ci>
1572
+ <ci> KiADPHK1 </ci>
1573
+ </apply>
1574
+ </apply>
1575
+ <apply>
1576
+ <plus/>
1577
+ <cn type="integer"> 1 </cn>
1578
+ <apply>
1579
+ <divide/>
1580
+ <ci> G6Pcyt </ci>
1581
+ <ci> KiG6PHK1 </ci>
1582
+ </apply>
1583
+ </apply>
1584
+ </apply>
1585
+ </apply>
1586
+ <apply>
1587
+ <divide/>
1588
+ <apply>
1589
+ <times/>
1590
+ <apply>
1591
+ <divide/>
1592
+ <ci> VmaxGK </ci>
1593
+ <cn type="integer"> 2 </cn>
1594
+ </apply>
1595
+ <apply>
1596
+ <divide/>
1597
+ <apply>
1598
+ <times/>
1599
+ <ci> Glucosecyt </ci>
1600
+ <ci> ATPcyt </ci>
1601
+ </apply>
1602
+ <apply>
1603
+ <times/>
1604
+ <ci> KmGlucoseHK2 </ci>
1605
+ <ci> KmATPHK2 </ci>
1606
+ </apply>
1607
+ </apply>
1608
+ </apply>
1609
+ <apply>
1610
+ <times/>
1611
+ <apply>
1612
+ <plus/>
1613
+ <cn type="integer"> 1 </cn>
1614
+ <apply>
1615
+ <divide/>
1616
+ <ci> Glucosecyt </ci>
1617
+ <ci> KmGlucoseHK2 </ci>
1618
+ </apply>
1619
+ <apply>
1620
+ <divide/>
1621
+ <ci> Fructose </ci>
1622
+ <ci> KmFructoseHK2 </ci>
1623
+ </apply>
1624
+ </apply>
1625
+ <apply>
1626
+ <plus/>
1627
+ <cn type="integer"> 1 </cn>
1628
+ <apply>
1629
+ <divide/>
1630
+ <ci> ATPcyt </ci>
1631
+ <ci> KmATPHK2 </ci>
1632
+ </apply>
1633
+ <apply>
1634
+ <divide/>
1635
+ <ci> ADPcyt </ci>
1636
+ <ci> KiADPHK2 </ci>
1637
+ </apply>
1638
+ </apply>
1639
+ </apply>
1640
+ </apply>
1641
+ </apply>
1642
+ </math>
1643
+ </kineticLaw>
1644
+ </reaction>
1645
+ <reaction id="vNDPK" name="vNDPK">
1646
+ <listOfReactants>
1647
+ <speciesReference species="ATPcyt"/>
1648
+ <speciesReference species="UDPcyt"/>
1649
+ </listOfReactants>
1650
+ <listOfProducts>
1651
+ <speciesReference species="ADPcyt"/>
1652
+ <speciesReference species="UTPcyt"/>
1653
+ </listOfProducts>
1654
+ <kineticLaw>
1655
+ <math xmlns="http://www.w3.org/1998/Math/MathML">
1656
+ <apply>
1657
+ <times/>
1658
+ <ci> VNDPK </ci>
1659
+ <apply>
1660
+ <minus/>
1661
+ <apply>
1662
+ <times/>
1663
+ <ci> kforwardNDPK </ci>
1664
+ <ci> ATPcyt </ci>
1665
+ <ci> UDPcyt </ci>
1666
+ </apply>
1667
+ <apply>
1668
+ <times/>
1669
+ <ci> kbackwardNDPK </ci>
1670
+ <ci> ADPcyt </ci>
1671
+ <ci> UTPcyt </ci>
1672
+ </apply>
1673
+ </apply>
1674
+ </apply>
1675
+ </math>
1676
+ </kineticLaw>
1677
+ </reaction>
1678
+ <reaction id="vAT" name="vAT">
1679
+ <listOfReactants>
1680
+ <speciesReference species="ADPam"/>
1681
+ <speciesReference species="ATPcyt"/>
1682
+ </listOfReactants>
1683
+ <listOfProducts>
1684
+ <speciesReference species="ATPam"/>
1685
+ <speciesReference species="ADPcyt"/>
1686
+ </listOfProducts>
1687
+ <kineticLaw>
1688
+ <math xmlns="http://www.w3.org/1998/Math/MathML">
1689
+ <apply>
1690
+ <times/>
1691
+ <ci> VAT </ci>
1692
+ <apply>
1693
+ <minus/>
1694
+ <apply>
1695
+ <times/>
1696
+ <ci> kforwardAT </ci>
1697
+ <ci> ATPcyt </ci>
1698
+ <ci> ADPam </ci>
1699
+ </apply>
1700
+ <apply>
1701
+ <times/>
1702
+ <ci> kbackwardAT </ci>
1703
+ <ci> ATPam </ci>
1704
+ <ci> ADPcyt </ci>
1705
+ </apply>
1706
+ </apply>
1707
+ </apply>
1708
+ </math>
1709
+ </kineticLaw>
1710
+ </reaction>
1711
+ <reaction id="vPexp" name="vPexp">
1712
+ <listOfReactants>
1713
+ <speciesReference species="Pam"/>
1714
+ </listOfReactants>
1715
+ <listOfProducts>
1716
+ <speciesReference species="Pcyt"/>
1717
+ </listOfProducts>
1718
+ <kineticLaw>
1719
+ <math xmlns="http://www.w3.org/1998/Math/MathML">
1720
+ <apply>
1721
+ <times/>
1722
+ <ci> VPexp </ci>
1723
+ <apply>
1724
+ <minus/>
1725
+ <apply>
1726
+ <times/>
1727
+ <ci> kforwardPexp </ci>
1728
+ <ci> Pam </ci>
1729
+ </apply>
1730
+ <apply>
1731
+ <times/>
1732
+ <ci> kbackwardPexp </ci>
1733
+ <ci> Pcyt </ci>
1734
+ </apply>
1735
+ </apply>
1736
+ </apply>
1737
+ </math>
1738
+ </kineticLaw>
1739
+ </reaction>
1740
+ <reaction id="vATPcons" name="vATPcons">
1741
+ <listOfReactants>
1742
+ <speciesReference species="ATPcyt"/>
1743
+ </listOfReactants>
1744
+ <listOfProducts>
1745
+ <speciesReference species="ADPcyt"/>
1746
+ <speciesReference species="Pcyt"/>
1747
+ </listOfProducts>
1748
+ <kineticLaw>
1749
+ <math xmlns="http://www.w3.org/1998/Math/MathML">
1750
+ <apply>
1751
+ <times/>
1752
+ <ci> VATPcons </ci>
1753
+ <ci> kATPcons </ci>
1754
+ <apply>
1755
+ <divide/>
1756
+ <ci> ATPcyt </ci>
1757
+ <ci> ADPcyt </ci>
1758
+ </apply>
1759
+ </apply>
1760
+ </math>
1761
+ </kineticLaw>
1762
+ </reaction>
1763
+ </listOfReactions>
1764
+ </model></sbml>