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Team:Paris Saclay/modeling/fnr0.xml
From 2013.igem.org
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<molecule name="FNR" quantity="5000"/> | <molecule name="FNR" quantity="5000"/> | ||
| - | <molecule name="O2" const="true" adjustable="true" quantity=" | + | <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 --> | ||
| Line 50: | Line 50: | ||
<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> | ||
| Line 70: | Line 70: | ||
<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="0.00001"> | <reaction probability="0.00001"> | ||
| - | <in> | + | <in>PV</in> |
</reaction> | </reaction> | ||
<reaction probability="0.00001"> | <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>
