Team:Paris Saclay/modeling/fnr0.xml

From 2013.igem.org

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<!-- Molecule declaration curve_show="true" curve_color="#AAAA00" -->
<!-- Molecule declaration curve_show="true" curve_color="#AAAA00" -->
-
<molecule name="FNR" quantity="10000"  adjustable="true"/>
+
<molecule name="FNR" quantity="5000"/>
-
<molecule name="O2" const="true" adjustable="true" quantity="50000"/>
+
<molecule name="O2" const="true" adjustable="true" quantity="5000"/>
-
<molecule name="FNR_ox"  adjustable="true"/>
+
<molecule name="FNR_ox" />
-
<molecule name="Pfnr_activator" quantity="1" adjustable="true"/>
+
<molecule name="Pfnr_activator" quantity="1"/>
-
<molecule name="Pfnr_activator_bond" adjustable="true"/>
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<molecule name="Pfnr_activator_bond"/>
-
<molecule name="GP" curve_show="true" curve_color="#00AA00" adjustable="true"/>
+
<molecule name="PV" curve_show="true" curve_color="#00AA00"/>
-
<molecule name="Pfnr_repressor" quantity="1" adjustable="true"/>
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<molecule name="Pfnr_repressor" quantity="1"/>
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<molecule name="Pfnr_repressor_bond" adjustable="true"/>
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<molecule name="Pfnr_repressor_bond"/>
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<molecule name="BP" curve_show="true" curve_color="#0000FF" adjustable="true"/>
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<molecule name="PR" curve_show="true" curve_color="#FF0000"/>
<!-- FNR oxydation -->
<!-- FNR oxydation -->
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<reaction probability="0.8">
+
<reaction probability="0.9">
  <in>FNR</in>
  <in>FNR</in>
  <in>O2</in>
  <in>O2</in>
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</reaction>
</reaction>
<!-- FNR reduction -->
<!-- FNR reduction -->
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<reaction probability="0.002">
+
<reaction probability="0.0001">
  <in>FNR_ox</in>
  <in>FNR_ox</in>
  <out>O2</out>
  <out>O2</out>
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<!-- Activating promoter bonding -->
<!-- Activating promoter bonding -->
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<reaction probability="2">
+
<reaction probability="0.9">
  <in>FNR</in>
  <in>FNR</in>
  <in>Pfnr_activator</in>
  <in>Pfnr_activator</in>
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</reaction>
</reaction>
<!-- Activating promoter unbonding -->
<!-- Activating promoter unbonding -->
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<reaction probability="0.005">
+
<reaction probability="0.001">
  <in>Pfnr_activator_bond</in>
  <in>Pfnr_activator_bond</in>
  <out>Pfnr_activator</out>
  <out>Pfnr_activator</out>
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</reaction>
</reaction>
<!-- Green reporter protein production -->
<!-- Green reporter protein production -->
-
<reaction probability="0.02">
+
<reaction probability="0.01">
  <in>Pfnr_activator_bond</in>
  <in>Pfnr_activator_bond</in>
  <out>Pfnr_activator_bond</out>
  <out>Pfnr_activator_bond</out>
-
  <out>GP</out>
+
  <out>PV</out>
</reaction>
</reaction>
<!-- Repressor bonding -->
<!-- Repressor bonding -->
-
<reaction probability="2">
+
<reaction probability="0.8">
  <in>FNR</in>
  <in>FNR</in>
  <in>Pfnr_repressor</in>
  <in>Pfnr_repressor</in>
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</reaction>
</reaction>
<!-- Blue reporter protein production -->
<!-- Blue reporter protein production -->
-
<reaction probability="0.02">
+
<reaction probability="0.01">
  <in>Pfnr_repressor</in>
  <in>Pfnr_repressor</in>
  <out>Pfnr_repressor</out>
  <out>Pfnr_repressor</out>
-
  <out>BP</out>
+
  <out>PR</out>
</reaction>
</reaction>
<!-- Reporter degradation -->
<!-- Reporter degradation -->
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<reaction probability="0.0001">
+
<reaction probability="0.00001">
-
  <in>GP</in>
+
  <in>PV</in>
</reaction>
</reaction>
-
<reaction probability="0.0001">
+
<reaction probability="0.00001">
-
  <in>BP</in>
+
  <in>PR</in>
</reaction>
</reaction>
</sim>
</sim>

Latest revision as of 23:53, 4 October 2013

<?xml version="1.0" encoding="ISO-8859-1"?>

<sim>

<yscale>1300</yscale>

<volume>0.7</volume> <timestep>0.0001</timestep> <alpha>7.4e-7</alpha>


<molecule name="FNR" quantity="5000"/> <molecule name="O2" const="true" adjustable="true" quantity="5000"/> <molecule name="FNR_ox" /> <molecule name="Pfnr_activator" quantity="1"/> <molecule name="Pfnr_activator_bond"/> <molecule name="PV" curve_show="true" curve_color="#00AA00"/> <molecule name="Pfnr_repressor" quantity="1"/> <molecule name="Pfnr_repressor_bond"/> <molecule name="PR" curve_show="true" curve_color="#FF0000"/>

<reaction probability="0.9"> 

<in>FNR</in>
<in>O2</in>
<out>FNR_ox</out>

</reaction> <reaction probability="0.0001"> 

<in>FNR_ox</in>
<out>O2</out>
<out>FNR</out>

</reaction>

<reaction probability="0.9"> 

<in>FNR</in>
<in>Pfnr_activator</in>
<out>Pfnr_activator_bond</out>

</reaction> <reaction probability="0.001"> 

<in>Pfnr_activator_bond</in>
<out>Pfnr_activator</out>
<out>FNR</out>

</reaction> <reaction probability="0.01"> 

<in>Pfnr_activator_bond</in>
<out>Pfnr_activator_bond</out>
<out>PV</out>

</reaction>


<reaction probability="0.8"> 

<in>FNR</in>
<in>Pfnr_repressor</in>
<out>Pfnr_repressor_bond</out>

</reaction> <reaction probability="0.001"> 

<in>Pfnr_repressor_bond</in>
<out>Pfnr_repressor</out>
<out>FNR</out>

</reaction> <reaction probability="0.01"> 

<in>Pfnr_repressor</in>
<out>Pfnr_repressor</out>
<out>PR</out>

</reaction>

<reaction probability="0.00001"> 

<in>PV</in>

</reaction> <reaction probability="0.00001"> 

<in>PR</in>

</reaction>

</sim>

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