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spirallus_model_level_2.fml
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spirallus_model_level_2.fml
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<?xml version="1.0" encoding="utf-8" standalone="no"?><fluxml xmlns="http://www.13cflux.net/fluxml" xmlns:xsi="http://www.w3.org/2001/XMLSchema-instance" xsi:schemaLocation="http://www.13cflux.net/fluxml http://www.13cflux.net/fluxml">
<info>
<version>1.1</version>
<comment>KN: Spirallus-Example With MS measurements</comment>
</info>
<reactionnetwork>
<metabolitepools>
<pool atoms="2" id="A"/>
<pool atoms="2" id="B"/>
<pool atoms="4" id="C"/>
<pool atoms="3" id="D"/>
<pool atoms="2" id="E"/>
<pool atoms="1" id="G"/>
<pool atoms="1" id="F"/>
<pool atoms="2" id="H"/>
</metabolitepools>
<reaction bidirectional="false" id="v1">
<reduct cfg="C#1@1 C#2@1" id="A"/>
<rproduct cfg="C#1@1 C#2@1" id="B"/>
</reaction>
<reaction bidirectional="false" id="v6">
<reduct cfg="C#1@1 C#2@1 C#3@1" id="D"/>
<rproduct cfg="C#1@1 C#2@1" id="E"/>
<rproduct cfg="C#3@1" id="G"/>
</reaction>
<reaction bidirectional="true" id="v2">
<reduct cfg="C#1@1 C#2@1" id="B"/>
<rproduct cfg="C#1@1 C#2@1" id="E"/>
</reaction>
<reaction bidirectional="false" id="v3">
<reduct cfg="C#1@1 C#2@1" id="B"/>
<reduct cfg="C#1@2 C#2@2" id="E"/>
<rproduct cfg="C#1@1 C#2@1 C#1@2 C#2@2" id="C"/>
</reaction>
<reaction bidirectional="false" id="v5">
<reduct cfg="C#1@1 C#2@1 C#3@1 C#4@1" id="C"/>
<rproduct cfg="C#2@1 C#3@1 C#4@1" id="D"/>
<rproduct cfg="C#1@1" id="F"/>
</reaction>
<reaction bidirectional="false" id="v4">
<reduct cfg="C#1@1 C#2@1" id="E"/>
<rproduct cfg="C#1@1 C#2@1" id="H"/>
</reaction>
<reaction id="h_ouz">
<reduct cfg="C#1@1 C#2@1" id="H"/>
</reaction>
<reaction id="g_ouz">
<reduct cfg="C#1@1" id="G"/>
</reaction>
<reaction id="f_out">
<reduct cfg="C#1@1" id="F"/>
</reaction>
</reactionnetwork>
<constraints>
<net>
<textual>
v1<= 100;
v1>= 1;
v2<= 70;
v2>= 0.7;
v2<=v1;
</textual>
</net>
<xch>
<textual>
v2<= 1;
v2>= 0.01;
</textual>
</xch>
<psize>
<textual>
B<= 100;
B>= 0.0001;
C<= 100;
C>= 0.0001;
D<= 100;
D>= 0.0001;
E<= 100;
E>= 0.0001;
F<= 100;
F>= 0.0001;
G<= 100;
G>= 0.0001;
H<= 100;
H>= 0.0001;
</textual>
</psize>
</constraints>
<configuration name="default" stationary="false" time="50">
<comment>spirallus synthetic measurement data</comment>
<input pool="A" type="isotopomer">
<label cfg="10" purity="0.99">0.1</label>
<label cfg="11" purity="0.99">0.9</label>
</input>
<measurement>
<model>
<labelingmeasurement>
<group id="ms_group_1" scale="auto" times="1.5,4,6.5,8,10,20">
<textual>C[1-2,4]#M0,1,2,3</textual>
</group>
<group id="ms_group_2" scale="auto" times="1.5,4,6.5,8,10,20">
<textual>B[1,2]#M0,1,2</textual>
</group>
<group id="ms_group_3" scale="one" times="1.5,4,6.5,8,10,20">
<textual>E[1,2]#M0,1,2</textual>
</group>
</labelingmeasurement>
</model>
<data>
<datum id="ms_group_1" stddev="0.001" time="1.5" weight="0">.3944812502157005</datum>
<datum id="ms_group_1" stddev="0.001" time="1.5" weight="1">.39213595942762747</datum>
<datum id="ms_group_1" stddev="0.001" time="1.5" weight="2">.18793504481625237</datum>
<datum id="ms_group_1" stddev="0.001" time="1.5" weight="3">.03259579734377384</datum>
<datum id="ms_group_1" stddev="0.001" time="4" weight="0">.06887428333759157</datum>
<datum id="ms_group_1" stddev="0.001" time="4" weight="1">.3159806346776769</datum>
<datum id="ms_group_1" stddev="0.001" time="4" weight="2">.4676055999539298</datum>
<datum id="ms_group_1" stddev="0.001" time="4" weight="3">.12300796473248234</datum>
<datum id="ms_group_1" stddev="0.001" time="6.5" weight="0">.022363373519724637</datum>
<datum id="ms_group_1" stddev="0.001" time="6.5" weight="1">.208132993570771</datum>
<datum id="ms_group_1" stddev="0.001" time="6.5" weight="2">.5502226538801799</datum>
<datum id="ms_group_1" stddev="0.001" time="6.5" weight="3">.19099405118352722</datum>
<datum id="ms_group_1" stddev="0.001" time="8" weight="0">.022363373519724637</datum>
<datum id="ms_group_1" stddev="0.001" time="8" weight="1">.208132993570771</datum>
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<datum id="ms_group_1" stddev="0.001" time="10" weight="0">.022363373519724637</datum>
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<datum id="ms_group_1" stddev="0.001" time="10" weight="3">.19099405118352722</datum>
<datum id="ms_group_1" stddev="0.001" time="20" weight="0">.022363373519724637</datum>
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<datum id="ms_group_1" stddev="0.001" time="20" weight="2">.5502226538801799</datum>
<datum id="ms_group_1" stddev="0.001" time="20" weight="3">.19099405118352722</datum>
<datum id="ms_group_2" stddev="0.001" time="1.5" weight="0">.2519855430395166</datum>
<datum id="ms_group_2" stddev="0.001" time="1.5" weight="1">.6150958770328989</datum>
<datum id="ms_group_2" stddev="0.001" time="1.5" weight="2">.07159673646341977</datum>
<datum id="ms_group_2" stddev="0.001" time="4" weight="0">.12074937271998513</datum>
<datum id="ms_group_2" stddev="0.001" time="4" weight="1">.7357157241336526</datum>
<datum id="ms_group_2" stddev="0.001" time="4" weight="2">.09622202129460586</datum>
<datum id="ms_group_2" stddev="0.001" time="6.5" weight="0">.08553267809239648</datum>
<datum id="ms_group_2" stddev="0.001" time="6.5" weight="1">.7647670399774833</datum>
<datum id="ms_group_2" stddev="0.001" time="6.5" weight="2">.11344858197054312</datum>
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<datum id="ms_group_2" stddev="0.001" time="10" weight="0">.08553267809239648</datum>
<datum id="ms_group_2" stddev="0.001" time="10" weight="1">.7647670399774833</datum>
<datum id="ms_group_2" stddev="0.001" time="10" weight="2">.11344858197054312</datum>
<datum id="ms_group_2" stddev="0.001" time="20" weight="0">.08553267809239648</datum>
<datum id="ms_group_2" stddev="0.001" time="20" weight="1">.7647670399774833</datum>
<datum id="ms_group_2" stddev="0.001" time="20" weight="2">.11344858197054312</datum>
<datum id="ms_group_3" stddev="0.001" time="1.5" weight="0">.5336075626878626</datum>
<datum id="ms_group_3" stddev="0.001" time="1.5" weight="1">.408439833891252</datum>
<datum id="ms_group_3" stddev="0.001" time="1.5" weight="2">.04662684589445842</datum>
<datum id="ms_group_3" stddev="0.001" time="4" weight="0">.2416273255910798</datum>
<datum id="ms_group_3" stddev="0.001" time="4" weight="1">.6548831029532279</datum>
<datum id="ms_group_3" stddev="0.001" time="4" weight="2">.11408956597276508</datum>
<datum id="ms_group_3" stddev="0.001" time="6.5" weight="0">.15466795662924404</datum>
<datum id="ms_group_3" stddev="0.001" time="6.5" weight="1">.699743719755679</datum>
<datum id="ms_group_3" stddev="0.001" time="6.5" weight="2">.15898170825561733</datum>
<datum id="ms_group_3" stddev="0.001" time="8" weight="0">.15466795662924404</datum>
<datum id="ms_group_3" stddev="0.001" time="8" weight="1">.699743719755679</datum>
<datum id="ms_group_3" stddev="0.001" time="8" weight="2">.15898170825561733</datum>
<datum id="ms_group_3" stddev="0.001" time="10" weight="0">.15466795662924404</datum>
<datum id="ms_group_3" stddev="0.001" time="10" weight="1">.699743719755679</datum>
<datum id="ms_group_3" stddev="0.001" time="10" weight="2">.15898170825561733</datum>
<datum id="ms_group_3" stddev="0.001" time="20" weight="0">.15466795662924404</datum>
<datum id="ms_group_3" stddev="0.001" time="20" weight="1">.699743719755679</datum>
<datum id="ms_group_3" stddev="0.001" time="20" weight="2">.15898170825561733</datum>
</data>
</measurement>
<simulation method="auto" type="full">
<variables>
<fluxvalue flux="v1" type="net">1.0</fluxvalue>
<fluxvalue flux="v2" type="net">.7</fluxvalue>
<fluxvalue flux="v2" type="xch">0.4</fluxvalue>
<poolsizevalue pool="B">1</poolsizevalue>
<poolsizevalue pool="C">0.1</poolsizevalue>
<poolsizevalue pool="D">20</poolsizevalue>
<poolsizevalue pool="E">0.1</poolsizevalue>
<poolsizevalue pool="F">1</poolsizevalue>
<poolsizevalue pool="G">1</poolsizevalue>
<poolsizevalue pool="H">1</poolsizevalue>
</variables>
</simulation>
</configuration>
</fluxml><!-- vim:set shiftwidth=2:set expandtab: -->