- Author:
- David Nickerson <nickerso@users.sourceforge.net>
- Date:
- 2015-02-16 16:45:16+13:00
- Desc:
- adding a second dummy uniprot annotation for testing; now using the located_in property from the OBO Relationship Ontology to annotate a components cellular location (idea from Mikes document) rather than abusing the encapsulation grouping in the CellML model
- Permanent Source URI:
- https://models.cellml.org/workspace/19f/rawfile/b6ee456100c3f0e68d9c59d4935f9a62f1b55f9a/passive-flux-equation/model.xml
<?xml version="1.0"?>
<model xmlns="http://www.cellml.org/cellml/1.1#" name="model"
xmlns:cellml="http://www.cellml.org/cellml/1.1#" xmlns:cmeta="http://www.cellml.org/metadata/2.0#"
cmeta:id="model" xmlns:xlink="http://www.w3.org/1999/xlink">
<!-- import the units that we want to use -->
<import xlink:href="../units/units-map.xml">
<units name="potential" units_ref="potential" />
<units name="concentration" units_ref="concentration" />
<units name="soluteFlux" units_ref="soluteFlux" />
<units name="permeability" units_ref="permeability" />
<units name="current" units_ref="current" />
<units name="membraneAreaFraction" units_ref="membraneAreaFraction" />
<units name="cellVolumeFraction" units_ref="cellVolumeFraction" />
<units name="hydraulicConductance" units_ref="hydraulicConductance" />
<units name="gas_constant" units_ref="gas_constant" />
<units name="faradays_constant" units_ref="faradays_constant" />
<units name="temperature" units_ref="temperature" />
<units name="time" units_ref="time" />
</import>
<component name="interface" cmeta:id="passiveFluxComponent">
<variable name="J" cmeta:id="J" units="soluteFlux"
public_interface="out" />
<variable name="P" cmeta:id="P" units="permeability"
public_interface="in" />
<variable name="z" cmeta:id="z" units="dimensionless"
public_interface="in" />
<variable name="E" cmeta:id="E" units="potential"
public_interface="in" />
<variable name="F" cmeta:id="F" units="faradays_constant"
public_interface="in" />
<variable name="R" cmeta:id="R" units="gas_constant"
public_interface="in" />
<variable name="T" cmeta:id="T" units="temperature"
public_interface="in" />
<variable name="C1" cmeta:id="C1" units="concentration"
public_interface="in" />
<variable name="C2" cmeta:id="C2" units="concentration"
public_interface="in" />
<variable name="zeroTolerance" cmeta:id="zeroTolerance"
initial_value="1.0e-4" units="soluteFlux" public_interface="out" />
<math xmlns="http://www.w3.org/1998/Math/MathML">
<apply>
<eq />
<ci>J</ci>
<piecewise>
<piece>
<apply>
<times />
<ci>P</ci>
<ci>z</ci>
<ci>E</ci>
<apply>
<divide />
<ci>F</ci>
<apply>
<times />
<ci>R</ci>
<ci>T</ci>
</apply>
</apply>
<apply>
<divide />
<apply>
<minus />
<ci>C1</ci>
<apply>
<times />
<ci>C2</ci>
<apply>
<exp />
<apply>
<minus />
<apply>
<times />
<ci>z</ci>
<ci>E</ci>
<apply>
<divide />
<ci>F</ci>
<apply>
<times />
<ci>R</ci>
<ci>T</ci>
</apply>
</apply>
</apply>
</apply>
</apply>
</apply>
</apply>
<apply>
<minus />
<cn cellml:units="dimensionless">1.0</cn>
<apply>
<exp />
<apply>
<minus />
<apply>
<times />
<ci>z</ci>
<ci>E</ci>
<apply>
<divide />
<ci>F</ci>
<apply>
<times />
<ci>R</ci>
<ci>T</ci>
</apply>
</apply>
</apply>
</apply>
</apply>
</apply>
</apply>
</apply>
<apply>
<gt />
<apply>
<abs />
<apply>
<times />
<ci>z</ci>
<ci>E</ci>
<apply>
<divide />
<ci>F</ci>
<apply>
<times />
<ci>R</ci>
<ci>T</ci>
</apply>
</apply>
</apply>
</apply>
<ci>zeroTolerance</ci>
</apply>
</piece>
<otherwise>
<apply>
<times />
<ci>P</ci>
<ci>z</ci>
<apply>
<divide />
<ci>F</ci>
<apply>
<times />
<ci>R</ci>
<ci>T</ci>
</apply>
</apply>
<apply>
<minus />
<ci>C1</ci>
<ci>C2</ci>
</apply>
</apply>
</otherwise>
</piecewise>
</apply>
</math>
</component>
</model>
