- Author:
- David Nickerson <nickerso@users.sourceforge.net>
- Date:
- 2011-05-04 15:55:57+12:00
- Desc:
- updating to an initial attempt at modularising this model. Have now defined a single model representing the single cell equations and then a second model which represents the two cell variant of the Collier et al (1996). the 2cell model imports the single cell model twice and defines the appropriate neighbourhood average values to pass into each of the single cell instances. The figure is the same as before, but regenerated from the new version of the model.
- Permanent Source URI:
- https://models.cellml.org/w/andre/DeltaNotch/rawfile/7ceb66207e12c1099988ff309103508f333da2ba/collier-2cell.xml
<?xml version="1.0" encoding="iso-8859-1"?>
<model name="DeltaNotch" cmeta:id="DeltaNotchModel"
xmlns="http://www.cellml.org/cellml/1.1#" xmlns:cellml="http://www.cellml.org/cellml/1.1#"
xmlns:cmeta="http://www.cellml.org/metadata/1.0#" xmlns:xlink="http://www.w3.org/1999/xlink">
<rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#"
xmlns:cmeta="http://www.cellml.org/metadata/1.0#" xmlns:bqs="http://www.cellml.org/bqs/1.0#"
xmlns:dc="http://purl.org/dc/elements/1.1/" xmlns:dcterms="http://purl.org/dc/terms/"
xmlns:vCard="http://www.w3.org/2001/vcard-rdf/3.0#" xmlns:cs="http://www.cellml.org/metadata/simulation/1.0#"
xmlns:cg="http://www.cellml.org/metadata/graphs/1.0#">
<rdf:Description rdf:about="#DeltaNotchModel">
<cs:simulation>
<rdf:Description rdf:ID="simulation">
<cs:multistepMethod>bdf</cs:multistepMethod>
<cs:iterationMethod>newton</cs:iterationMethod>
<cs:linearSolver>dense</cs:linearSolver>
<cs:boundIntervals rdf:parseType="Collection">
<rdf:Description>
<cs:boundVariable>
<rdf:Description rdf:about="#time" />
</cs:boundVariable>
<cs:maximumStepSize rdf:datatype="http://www.w3.org/2001/XMLSchema#double">
0.01
</cs:maximumStepSize>
<cs:tabulationStepSize rdf:datatype="http://www.w3.org/2001/XMLSchema#double">
0.1
</cs:tabulationStepSize>
<cs:startingValue rdf:datatype="http://www.w3.org/2001/XMLSchema#double">
0
</cs:startingValue>
<cs:endingValue rdf:datatype="http://www.w3.org/2001/XMLSchema#double">
25
</cs:endingValue>
</rdf:Description>
</cs:boundIntervals>
</rdf:Description>
</cs:simulation>
</rdf:Description>
<rdf:Description>
<cg:graph>
<rdf:Description rdf:ID="collier-2cell-graph">
<cg:x-label>Time</cg:x-label>
<cg:y-label>value</cg:y-label>
<cg:background-colour>#ffffff</cg:background-colour>
<cg:traces rdf:parseType="Collection">
<rdf:Description>
<cg:label>n1</cg:label>
<cg:type rdf:resource="http://www.cellml.org/metadata/graphs/1.0#line" />
<cg:colour>#ff0000</cg:colour>
<cg:x-variable rdf:parseType="Resource">
<cs:simulation rdf:resource="#simulation" />
<cg:variable rdf:resource="#time" />
</cg:x-variable>
<cg:y-variable rdf:parseType="Resource">
<cs:simulation rdf:resource="#simulation" />
<cg:variable rdf:resource="#n1" />
</cg:y-variable>
</rdf:Description>
<rdf:Description>
<cg:label>n2</cg:label>
<cg:type rdf:resource="http://www.cellml.org/metadata/graphs/1.0#line" />
<cg:colour>#0000ff</cg:colour>
<cg:x-variable rdf:parseType="Resource">
<cs:simulation rdf:resource="#simulation" />
<cg:variable rdf:resource="#time" />
</cg:x-variable>
<cg:y-variable rdf:parseType="Resource">
<cs:simulation rdf:resource="#simulation" />
<cg:variable rdf:resource="#n2" />
</cg:y-variable>
</rdf:Description>
<rdf:Description>
<cg:label>d1</cg:label>
<cg:type rdf:resource="http://www.cellml.org/metadata/graphs/1.0#line" />
<cg:colour>#008000</cg:colour>
<cg:x-variable rdf:parseType="Resource">
<cs:simulation rdf:resource="#simulation" />
<cg:variable rdf:resource="#time" />
</cg:x-variable>
<cg:y-variable rdf:parseType="Resource">
<cs:simulation rdf:resource="#simulation" />
<cg:variable rdf:resource="#d1" />
</cg:y-variable>
</rdf:Description>
<rdf:Description>
<cg:label>d2</cg:label>
<cg:type rdf:resource="http://www.cellml.org/metadata/graphs/1.0#line" />
<cg:colour>#000000</cg:colour>
<cg:x-variable rdf:parseType="Resource">
<cs:simulation rdf:resource="#simulation" />
<cg:variable rdf:resource="#time" />
</cg:x-variable>
<cg:y-variable rdf:parseType="Resource">
<cs:simulation rdf:resource="#simulation" />
<cg:variable rdf:resource="#d2" />
</cg:y-variable>
</rdf:Description>
</cg:traces>
</rdf:Description>
</cg:graph>
</rdf:Description>
</rdf:RDF>
<import xlink:href="single-cell.xml">
<component name="cell_1" component_ref="component" />
</import>
<import xlink:href="single-cell.xml">
<component name="cell_2" component_ref="component" />
</import>
<component name="component">
<variable cmeta:id="n1_initial" name="n1_initial" units="dimensionless"
initial_value="1.0" />
<variable cmeta:id="d1_initial" name="d1_initial" units="dimensionless"
initial_value="1.0" />
<variable cmeta:id="n2_initial" name="n2_initial" units="dimensionless"
initial_value="0.99" />
<variable cmeta:id="d2_initial" name="d2_initial" units="dimensionless"
initial_value="0.99" />
<variable cmeta:id="n1" name="n1" units="dimensionless"
public_interface="in" />
<variable cmeta:id="d1" name="d1" units="dimensionless"
public_interface="in" />
<variable cmeta:id="n2" name="n2" units="dimensionless"
public_interface="in" />
<variable cmeta:id="d2" name="d2" units="dimensionless"
public_interface="in" />
<variable cmeta:id="cell_1_neighbourhood_d_average" name="cell_1_neighbourhood_d_average"
units="dimensionless" public_interface="out" />
<variable cmeta:id="cell_2_neighbourhood_d_average" name="cell_2_neighbourhood_d_average"
units="dimensionless" public_interface="out" />
<variable cmeta:id="a" name="a" units="dimensionless"
initial_value="0.01" public_interface="out" />
<variable cmeta:id="b" name="b" units="dimensionless"
initial_value="100" public_interface="out" />
<variable cmeta:id="v" name="v" units="dimensionless"
initial_value="1" public_interface="out" />
<variable cmeta:id="k" name="k" units="dimensionless"
initial_value="2" public_interface="out" />
<variable cmeta:id="h" name="h" units="dimensionless"
initial_value="2" public_interface="out" />
<variable cmeta:id="time" name="time" units="dimensionless"
public_interface="out" />
<math xmlns="http://www.w3.org/1998/Math/MathML">
<apply>
<eq />
<ci>cell_1_neighbourhood_d_average</ci>
<apply>
<times />
<ci>d2</ci>
<cn cellml:units="dimensionless">0.5</cn>
</apply>
</apply>
<apply>
<eq />
<ci>cell_2_neighbourhood_d_average</ci>
<apply>
<times />
<ci>d1</ci>
<cn cellml:units="dimensionless">0.5</cn>
</apply>
</apply>
</math>
</component>
<connection>
<map_components component_1="component" component_2="cell_1"/>
<map_variables variable_1="n1" variable_2="n"/>
<map_variables variable_1="n1_initial" variable_2="n_initial"/>
<map_variables variable_1="d1" variable_2="d"/>
<map_variables variable_1="d1_initial" variable_2="d_initial"/>
<map_variables variable_1="cell_1_neighbourhood_d_average" variable_2="neighbourhood_d_average"/>
<map_variables variable_1="a" variable_2="a"/>
<map_variables variable_1="b" variable_2="b"/>
<map_variables variable_1="v" variable_2="v"/>
<map_variables variable_1="k" variable_2="k"/>
<map_variables variable_1="h" variable_2="h"/>
<map_variables variable_1="time" variable_2="time"/>
</connection>
<connection>
<map_components component_1="component" component_2="cell_2"/>
<map_variables variable_1="n2" variable_2="n"/>
<map_variables variable_1="n2_initial" variable_2="n_initial"/>
<map_variables variable_1="d2" variable_2="d"/>
<map_variables variable_1="d2_initial" variable_2="d_initial"/>
<map_variables variable_1="cell_2_neighbourhood_d_average" variable_2="neighbourhood_d_average"/>
<map_variables variable_1="a" variable_2="a"/>
<map_variables variable_1="b" variable_2="b"/>
<map_variables variable_1="v" variable_2="v"/>
<map_variables variable_1="k" variable_2="k"/>
<map_variables variable_1="h" variable_2="h"/>
<map_variables variable_1="time" variable_2="time"/>
</connection>
</model>
