Latest revision as of 08:09, 31 August 2015

<?xml version="1.0" encoding="UTF-8" standalone="yes" ?>
<!-- Simulation definition -->
<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>



    <!-- Generate yeast cells -->
    <!--
    <module name="object-generator">
        <object class="cell.Yeast" probability="0.1" growth-rate = ".02/s" velocity="400um/s 0" position-min="-190um -100um" position-max="-195um 100um" programs="cell1">
            <molecule name="LM3" amount="1000" />
            <molecule name="LM6" amount="1000" />
            <molecule name="BFP" amount="10" />
        </object>
        
        <object class="cell.Yeast" probability="0.1" growth-rate = ".02/s" velocity="400um/s 0" position-min="-190um -100um" position-max="-195um 100um" programs="cell2">
            <molecule name="LM4" amount="1000" />
            <molecule name="LM6" amount="1000" />
            <molecule name="BFP" amount="1000" />
        </object>
    </module>
-->

    <!-- Define streamlines -->
    <!--<module name="streamlines" grid="200 100" inlet-velocity="400um/s" dynamic-object-obstacles = "false"/>-->
    
  <!--  <module name = "streamlines-image" 
            access-name = "streamlines" 
            grid="100 100"
            dynamic-object-obstacles = "false"
            layout = "outlet none none inlet"
            inlet-velocity = "500um/s"
            obstacle="testtube2-01.png"
            image="testtubep-01.png"/>
            
    
    <module name="diffusion-streamlines" />
-->


    <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>

    <!-- Define diffusion 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>