Agglutination.cece

<?xml version="1.0" encoding="UTF-8" standalone="yes" ?>
<!-- Simulation definition -->
<simulation world-size="1000um 1000um" dt="1ms" background="white" length-coefficient="1e-1">

    <!--
    Simulation parameters.

    Can be changed by passing arguments to executable:
    $ ./cece-cli -p count 5000 -p ratio 0.3 Agglutination.cece
     -->
    <parameter name="count" value="2000" />
    <parameter name="ratio" value="0.5" />

    <plugin name="python" />
    <plugin name="agglutination" />
    <plugin name="cell" />
    <plugin name="obstacle" />

    <visualization>
        <layer name="physics" key="D" />
    </visualization>

    <!-- Define border walls -->
    <object class="obstacle.Rectangle" position="0um -500um" size="1000um 10um" visible="true" />
    <object class="obstacle.Rectangle" position="0um 500um" size="1000um 10um" visible="true" />
    <object class="obstacle.Rectangle" position="-500um 0um" size="10um 1000um" visible="true" />
    <object class="obstacle.Rectangle" position="500um 0um" size="10um 1000um" visible="true" />

    <module name="agglutination" >
        <bond association-constant="1000000" disassociation-constant="1" ligand="TAG_1" receptor="TAG_2" />
    </module>

    <!-- Define custom types with predefined molecules -->
    <type name="Yeast1" type="cell.Yeast">
        <molecule name="RFP" amount="1000" />
        <molecule name="TAG_1" amount="1000" />
    </type>

    <type name="Yeast2" type="cell.Yeast">
        <molecule name="GFP" amount="1000" />
        <molecule name="TAG_2" amount="1000" />
    </type>

    <!-- Generate cells at random places -->
    <init language="python">
<![CDATA[
import core
import random

x_ranges = [-190, 190]
y_ranges = [-190, 190]

def __call__(simulation):
    count = int(simulation.getParameter("count"))
    ratio = float(simulation.getParameter("ratio"))
    count1 = int(count * (1 - ratio))
    count2 = int(count * ratio)

    # Generate cell of the first type
    for i in xrange(1, count1):
        yeast = simulation.createObject("Yeast1")
        x = random.uniform(x_ranges[0], x_ranges[1])
        y = random.uniform(y_ranges[0], y_ranges[1])
        yeast.position = core.VectorPosition(x, y)

    # Generate cell of the second type
    for i in xrange(1, count2):
        yeast = simulation.createObject("Yeast2")
        x = random.uniform(x_ranges[0], x_ranges[1])
        y = random.uniform(y_ranges[0], y_ranges[1])
        yeast.position = core.VectorPosition(x, y)
]]>
    </init>

    <!-- Apply random forces to the cells each iteration -->
    <module name="brownian" language="python">
<![CDATA[
import core
import random

Fx_ranges = [-1e-4, 1e-4]
Fy_ranges = [-1e-4, 1e-4]

def update(dt, simulation):
    count = simulation.objectCount
    for i in xrange(0, count):
        object = simulation.getObject(i)
        Fx = random.uniform(Fx_ranges[0], Fx_ranges[1])
        Fy = random.uniform(Fy_ranges[0], Fy_ranges[1])
        object.applyForce(core.VectorForce(Fx, Fy))
]]>
    </module>

</simulation>