Team:Paris Saclay/modeling/fnr1.xml

From 2013.igem.org

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<sim>
<sim>
 +
 +
<yscale>1300</yscale>
<volume>0.7</volume> <!-- 0.7 micrometres cube -->
<volume>0.7</volume> <!-- 0.7 micrometres cube -->
Line 7: Line 9:
<alpha>7.4e-7</alpha> <!-- alpha -->
<alpha>7.4e-7</alpha> <!-- alpha -->
-
<molecule name="fnr" quantity="5000" curve_show="true" curve_color="#FF0000" adjustable="true"/>
+
<molecule name="PGV" quantity="50"/>
-
<molecule name="fnr_inactive" quantity="0" curve_show="true" curve_color="#0000FF" adjustable="true" />
+
<molecule name="PGVa"/>
-
<molecule name="O2" quantity="5000" const="true" adjustable="true" />
+
<molecule name="PGR" quantity="50"/>
 +
<molecule name="PGR1"/>
 +
<molecule name="PGR2"/>
 +
<molecule name="FNR" curve_show="true" curve_color="#0000FF" quantity="1226"/>
 +
<molecule name="FNRo"/>
 +
<molecule name="FNRoo"/>
 +
<molecule name="DFNR"/>
 +
<molecule name="DFNRa" curve_show="true" curve_color="#AAAA00"/>
 +
<molecule name="DFNR1"/>
 +
<molecule name="DFNR2"/>
 +
<molecule name="DFNR3"/>
 +
<molecule name="O2" const="true" adjustable="true" quantity="5000"/>
 +
<molecule name="PV" curve_show="true" curve_color="#00AA00"/>
 +
<molecule name="PR" curve_show="true" curve_color="#FF0000"/>
 +
<molecule name="DEG" quantity="100"/>
-
<reaction probability="0.002">
+
<!-- Dimerisation -->
-
  <in>fnr</in>
+
<reaction probability="0.05">
 +
<in>FNR</in>
 +
<in>FNR</in>
 +
<out>DFNRa</out>
 +
</reaction>
 +
 
 +
<!-- Oxydation -->
 +
<reaction probability="0.05">
 +
  <in>DFNRa</in>
  <in>O2</in>
  <in>O2</in>
-
  <out>fnr_inactive</out>
+
  <out>DFNR1</out>
 +
</reaction>
 +
<reaction probability="0.05">
 +
<in>DFNR1</in>
 +
<in>O2</in>
 +
<out>DFNR2</out>
 +
</reaction>
 +
<reaction probability="0.05">
 +
<in>DFNR2</in>
 +
<in>O2</in>
 +
<out>DFNR3</out>
 +
</reaction>
 +
<reaction probability="0.05">
 +
<in>DFNR3</in>
 +
<in>O2</in>
 +
<out>DFNR</out>
</reaction>
</reaction>
 +
<!-- Le complexe se defait -->
 +
<reaction probability="0.005">
 +
<in>DFNR</in>
 +
<out>FNRoo</out>
 +
<out>FNRoo</out>
 +
</reaction>
 +
<reaction probability="1">
 +
<in>FNRoo</in>
 +
<out>FNRo</out>
 +
<out>O2</out>
 +
</reaction>
 +
<reaction probability="1">
 +
<in>FNRo</in>
 +
<out>FNR</out>
 +
<out>O2</out>
 +
</reaction>
 +
 +
<!-- activation du gene vert -->
 +
<reaction probability="0.8">
 +
<in>PGV</in>
 +
<in>DFNRa</in>
 +
<out>PGVa</out>
 +
</reaction>
<reaction probability="0.0001">
<reaction probability="0.0001">
-
  <in>fnr_inactive</in>
+
  <in>PGVa</in>
-
  <out>fnr</out>
+
  <out>PGV</out>
 +
<out>DFNRa</out>
 +
</reaction>
 +
 
 +
<!-- le gene vert s'exprime -->
 +
<reaction probability="0.0001">
 +
<in>PGVa</in>
 +
<out>PGVa</out>
 +
<out>PV</out>
 +
</reaction>
 +
 
 +
<!-- repression du gene rouge -->
 +
<reaction probability="0.8">
 +
<in>PGR</in>
 +
<in>DFNRa</in>
 +
<out>PGR1</out>
 +
</reaction>
 +
<reaction probability="0.0001">
 +
<in>PGR1</in>
 +
<out>PGR</out>
 +
<out>DFNRa</out>
 +
</reaction>
 +
 
 +
<reaction probability="0.8">
 +
<in>PGR1</in>
 +
<in>DFNRa</in>
 +
<out>PGR2</out>
 +
</reaction>
 +
<reaction probability="0.0001">
 +
<in>PGR2</in>
 +
<out>PGR1</out>
 +
<out>DFNRa</out>
 +
</reaction>
 +
 
 +
<!--le gene rouge s'exprime quand rien n'est fixé -->
 +
<reaction probability="0.0001">
 +
<in>PGR</in>
 +
<out>PGR</out>
 +
<out>PR</out>
 +
</reaction>
 +
<reaction probability="0.0001">
 +
<in>PGR1</in>
 +
<out>PGR1</out>
 +
<out>PR</out>
 +
</reaction>
 +
 
 +
<!-- dégradation des protéines -->
 +
<reaction probability="0.1">
 +
<in>DEG</in>
 +
<in>PV</in>
 +
<out>DEG</out>
 +
</reaction>
 +
<reaction probability="0.1">
 +
<in>DEG</in>
 +
<in>PR</in>
 +
<out>DEG</out>
</reaction>
</reaction>
</sim>
</sim>

Latest revision as of 22:33, 13 August 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="PGV" quantity="50"/> <molecule name="PGVa"/> <molecule name="PGR" quantity="50"/> <molecule name="PGR1"/> <molecule name="PGR2"/> <molecule name="FNR" curve_show="true" curve_color="#0000FF" quantity="1226"/> <molecule name="FNRo"/> <molecule name="FNRoo"/> <molecule name="DFNR"/> <molecule name="DFNRa" curve_show="true" curve_color="#AAAA00"/> <molecule name="DFNR1"/> <molecule name="DFNR2"/> <molecule name="DFNR3"/> <molecule name="O2" const="true" adjustable="true" quantity="5000"/> <molecule name="PV" curve_show="true" curve_color="#00AA00"/> <molecule name="PR" curve_show="true" curve_color="#FF0000"/> <molecule name="DEG" quantity="100"/>

<reaction probability="0.05"> 

<in>FNR</in>
<in>FNR</in>
<out>DFNRa</out>

</reaction>

<reaction probability="0.05"> 

<in>DFNRa</in>
<in>O2</in>
<out>DFNR1</out>

</reaction> <reaction probability="0.05"> 

<in>DFNR1</in>
<in>O2</in>
<out>DFNR2</out>

</reaction> <reaction probability="0.05"> 

<in>DFNR2</in>
<in>O2</in>
<out>DFNR3</out>

</reaction> <reaction probability="0.05"> 

<in>DFNR3</in>
<in>O2</in>
<out>DFNR</out>

</reaction>

<reaction probability="0.005"> 

<in>DFNR</in>
<out>FNRoo</out>
<out>FNRoo</out>

</reaction> <reaction probability="1"> 

<in>FNRoo</in>
<out>FNRo</out>
<out>O2</out>

</reaction> <reaction probability="1"> 

<in>FNRo</in>
<out>FNR</out>
<out>O2</out>

</reaction>

<reaction probability="0.8"> 

<in>PGV</in>
<in>DFNRa</in>
<out>PGVa</out>

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

<in>PGVa</in>
<out>PGV</out>
<out>DFNRa</out>

</reaction>

<reaction probability="0.0001"> 

<in>PGVa</in>
<out>PGVa</out>
<out>PV</out>

</reaction>

<reaction probability="0.8"> 

<in>PGR</in>
<in>DFNRa</in>
<out>PGR1</out>

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

<in>PGR1</in>
<out>PGR</out>
<out>DFNRa</out>

</reaction>

<reaction probability="0.8"> 

<in>PGR1</in>
<in>DFNRa</in>
<out>PGR2</out>

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

<in>PGR2</in>
<out>PGR1</out>
<out>DFNRa</out>

</reaction>

<reaction probability="0.0001"> 

<in>PGR</in>
<out>PGR</out>
<out>PR</out>

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

<in>PGR1</in>
<out>PGR1</out>
<out>PR</out>

</reaction>

<reaction probability="0.1"> 

<in>DEG</in>
<in>PV</in>
<out>DEG</out>

</reaction> <reaction probability="0.1"> 

<in>DEG</in>
<in>PR</in>
<out>DEG</out>

</reaction>

</sim>

Retrieved from "http://2013.igem.org/Team:Paris_Saclay/modeling/fnr1.xml"