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=" | + | <molecule name="FNR" quantity="5000"/> |
<molecule name="O2" const="true" adjustable="true" quantity="5000"/> | <molecule name="O2" const="true" adjustable="true" quantity="5000"/> | ||
- | <molecule name="FNR_ox | + | <molecule name="FNR_ox" /> |
- | <molecule name="Pfnr_activator" quantity="1 | + | <molecule name="Pfnr_activator" quantity="1"/> |
- | <molecule name="Pfnr_activator_bond | + | <molecule name="Pfnr_activator_bond"/> |
- | <molecule name=" | + | <molecule name="PV" curve_show="true" curve_color="#00AA00"/> |
- | <molecule name="Pfnr_repressor" quantity="1 | + | <molecule name="Pfnr_repressor" quantity="1"/> |
- | <molecule name="Pfnr_repressor_bond | + | <molecule name="Pfnr_repressor_bond"/> |
- | <molecule name=" | + | <molecule name="PR" curve_show="true" curve_color="#FF0000"/> |
<!-- FNR oxydation --> | <!-- FNR oxydation --> | ||
- | <reaction probability="0. | + | <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 --> | ||
- | <reaction probability="0. | + | <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 --> | ||
- | <reaction probability="0. | + | <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 --> | ||
- | <reaction probability="0. | + | <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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<in>Pfnr_activator_bond</in> | <in>Pfnr_activator_bond</in> | ||
<out>Pfnr_activator_bond</out> | <out>Pfnr_activator_bond</out> | ||
- | <out> | + | <out>PV</out> |
</reaction> | </reaction> | ||
<!-- Repressor bonding --> | <!-- Repressor bonding --> | ||
- | <reaction probability="0. | + | <reaction probability="0.8"> |
<in>FNR</in> | <in>FNR</in> | ||
<in>Pfnr_repressor</in> | <in>Pfnr_repressor</in> | ||
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</reaction> | </reaction> | ||
<!-- Repressor unbonding --> | <!-- Repressor unbonding --> | ||
- | <reaction probability="0. | + | <reaction probability="0.001"> |
<in>Pfnr_repressor_bond</in> | <in>Pfnr_repressor_bond</in> | ||
<out>Pfnr_repressor</out> | <out>Pfnr_repressor</out> | ||
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<in>Pfnr_repressor</in> | <in>Pfnr_repressor</in> | ||
<out>Pfnr_repressor</out> | <out>Pfnr_repressor</out> | ||
- | <out> | + | <out>PR</out> |
</reaction> | </reaction> | ||
<!-- Reporter degradation --> | <!-- Reporter degradation --> | ||
- | <reaction probability="0. | + | <reaction probability="0.00001"> |
- | <in> | + | <in>PV</in> |
</reaction> | </reaction> | ||
- | <reaction probability="0. | + | <reaction probability="0.00001"> |
- | <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>