- Author:
- David Nickerson <nickerso@users.sourceforge.net>
- Date:
- 2011-05-09 10:04:07+12:00
- Desc:
- using CellML2Dot revealed that I had missed the public_interface attribute required on the initial value variables
- Permanent Source URI:
- https://models.fieldml.org/w/andre/DeltaNotch/rawfile/11ec11f15306a4bde9e649023d51364ba2a4423d/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" public_interface="out" />
<variable cmeta:id="d1_initial" name="d1_initial" units="dimensionless"
initial_value="1.0" public_interface="out" />
<variable cmeta:id="n2_initial" name="n2_initial" units="dimensionless"
initial_value="0.99" public_interface="out" />
<variable cmeta:id="d2_initial" name="d2_initial" units="dimensionless"
initial_value="0.99" public_interface="out" />
<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 name="start_boundary_d" initial_value="0.0" units="dimensionless"/>
<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" />
<variable name="start_boundary_d" initial_value="0.0" units="dimensionless"/>
<variable name="end_boundary_d" initial_value="0.0" units="dimensionless"/>
<math xmlns="http://www.w3.org/1998/Math/MathML">
<apply>
<eq />
<ci>cell_1_neighbourhood_d_average</ci>
<apply>
<times />
<apply><plus/>
<ci>d2</ci>
<ci>start_boundary_d</ci>
</apply>
<cn cellml:units="dimensionless">0.5</cn>
</apply>
</apply>
<apply>
<eq />
<ci>cell_2_neighbourhood_d_average</ci>
<apply>
<times />
<apply><plus/>
<ci>d1</ci>
<ci>end_boundary_d</ci>
</apply>
<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>
