Revision as of 10:15, 30 August 2015

<?xml version="1.0" encoding="UTF-8" standalone="yes" ?> <simulation world-size="100um 100um" dt="1ms" aiterations="1000" background="white">

   <parameter name="t1" value=".000001uM" />
   <parameter name="t2" value=".004uM" />
   <program name="cell1" language="stochastic-reactions-intercellular">

<![CDATA[

       if env_S2 > t1: null <.1, 1000 > LM5;
       if env_S2 > t1: null > 2000 > BFP;
       if env_S2 > t1: null > 20000 > env_S3;
       null > 1000 > env_S1;

]]>

   </program>
   
   <program name="cell2" language="stochastic-reactions-intercellular">

<![CDATA[

       if env_S1 > t2: null > 2000 > env_S2;
       if env_S1 > t2: null < .1, 1000 > LM5;

]]>

   </program>

   <module name="agglutination">
       <bond ligand="LM1" receptor="LM3" association-constant="100" disassociation-constant="0" />
       <bond ligand="LM2" receptor="LM4" association-constant="100" disassociation-constant="0" />
       <bond ligand="LM5" receptor="LM6" association-constant="100" disassociation-constant="0" />
       <bond ligand="LM7" receptor="LM8" association-constant="100" disassociation-constant="0" />
   </module>

   <module name="diffusion" grid="800 400">
       <signal name="S2" diffusion-rate="50um2/s" degradation-rate=".01/s" color = "red" saturation=".01uM" />
       <signal name="S1" diffusion-rate="50um2/s" degradation-rate=".01/s" color = "white" saturation=".01uM" />
       
       <signal name="S3" diffusion-rate="50um2/s" degradation-rate=".01/s" color = "green" saturation=".001uM" />
       
       
       
   </module>
   
   <object class="cell.Yeast" position="0um 0um" programs="cell1">
       <molecule name="LM3" amount="1000" />
       <molecule name="LM6" amount="1000" />
       <molecule name="BFP" amount="10" />
   </object>
   <object class="cell.Yeast" position="-4.5um 0um" programs="cell2">
       <molecule name="LM4" amount="1000" />
       <molecule name="LM6" amount="1000" />
       <molecule name="BFP" amount="100" />
   </object>
       

</simulation>