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spirallus_model_level_3.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: CN-Spirallus-Example With MS measurements</comment>
</info>
<reactionnetwork>
<metabolitepools>
<pool atoms="2" cfg="C1N1" id="A"/>
<pool atoms="2" cfg="C1N1" id="B"/>
<pool atoms="4" cfg="C2N2" id="C"/>
<pool atoms="3" cfg="C2N1" id="D"/>
<pool atoms="2" cfg="C1N1" id="E"/>
<pool atoms="1" cfg="C1N0" id="G"/>
<pool atoms="1" cfg="C0N1" id="F"/>
<pool atoms="2" cfg="C1N1" id="H"/>
</metabolitepools>
<reaction bidirectional="false" id="v1">
<reduct cfg="C#1@1 N#2@1" id="A"/>
<rproduct cfg="C#1@1 N#2@1" id="B"/>
</reaction>
<reaction bidirectional="false" id="v6">
<reduct cfg="C#1@1 C#2@1 N#3@1" id="D"/>
<rproduct cfg="C#2@1 N#3@1" id="E"/>
<rproduct cfg="C#1@1" id="G"/>
</reaction>
<reaction bidirectional="true" id="v2">
<reduct cfg="C#1@1 N#2@1" id="B"/>
<rproduct cfg="C#1@1 N#2@1" id="E"/>
</reaction>
<reaction bidirectional="false" id="v3">
<reduct cfg="C#1@1 N#2@1" id="B"/>
<reduct cfg="C#1@2 N#2@2" id="E"/>
<rproduct cfg="C#1@1 C#1@2 N#2@1 N#2@2" id="C"/>
</reaction>
<reaction bidirectional="false" id="v5">
<reduct cfg="C#1@1 C#2@1 N#3@1 N#4@1" id="C"/>
<rproduct cfg="C#1@1 C#2@1 N#3@1" id="D"/>
<rproduct cfg="N#4@1" id="F"/>
</reaction>
<reaction bidirectional="false" id="v4">
<reduct cfg="C#1@1 N#2@1" id="E"/>
<rproduct cfg="C#1@1 N#2@1" id="H"/>
</reaction>
<reaction bidirectional="false" id="h_ouz">
<annotation name="pathway"/>
<reduct cfg="C#1@1 N#2@1" id="H"/>
</reaction>
<reaction bidirectional="false" id="g_ouz">
<annotation name="pathway"/>
<reduct cfg="C#1@1" id="G"/>
</reaction>
<reaction bidirectional="false" id="f_out">
<annotation name="pathway"/>
<reduct cfg="N#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>
</constraints>
<configuration name="default" stationary="true">
<comment>spirallus synthetic CN measurement data</comment>
<input pool="A" type="isotopomer">
<label cfg="01" purity="0.99 0.88">0.98</label>
<label cfg="10" purity="0.77 0.66">0.02</label>
</input>
<measurement>
<model>
<labelingmeasurement>
<group id="gen_group_1" scale="auto">
<textual>B[1-2]#M(0,0),(0,1),(1,0),(1,1)</textual>
</group>
<group id="gen_group_2" scale="auto">
<textual>C[1-4]#M(0,0),(1,1),(2,2),(2,1)</textual>
</group>
</labelingmeasurement>
</model>
<data>
<datum id="gen_group_1" stddev="0.001" weight="0,0">.1244812502157005</datum>
<datum id="gen_group_1" stddev="0.001" weight="0,1">.56213595942762747</datum>
<datum id="gen_group_1" stddev="0.001" weight="1,0">.07898954578158745</datum>
<datum id="gen_group_1" stddev="0.001" weight="1,1">.1204887542762747</datum>
<datum id="gen_group_2" stddev="0.001" weight="0,0">.1244812502157005</datum>
<datum id="gen_group_2" stddev="0.001" weight="1,1">.56213595942762747</datum>
<datum id="gen_group_2" stddev="0.001" weight="2,2">.07898954578158745</datum>
<datum id="gen_group_2" stddev="0.001" weight="2,1">.1204887542762747</datum>
</data>
</measurement>
<simulation method="auto" type="auto">
<variables>
<fluxvalue flux="v1" type="net">1.0</fluxvalue>
<fluxvalue flux="v2" type="net">0.7</fluxvalue>
<fluxvalue flux="v2" type="xch">0.4</fluxvalue>
</variables>
</simulation>
</configuration>
</fluxml>