- Author:
- David Nickerson <nickerso@users.sourceforge.net>
- Date:
- 2018-01-10 16:06:43+13:00
- Desc:
- adding initial CellML and SEDML.
Slightly modified version of the model from my PhD thesis(https://doi.org/10.6084/m9.figshare.966660.v1).
- Permanent Source URI:
- https://models.physiomeproject.org/workspace/4f0/rawfile/7e4ab2db47e3c9bdb086201753bd559fb1a780f5/1998_nash.cellml
<?xml version='1.0'?>
<model cmeta:id="nash_1998" name="nash_1998" xmlns="http://www.cellml.org/cellml/1.0#" xmlns:cellml="http://www.cellml.org/cellml/1.0#" xmlns:cmeta="http://www.cellml.org/metadata/1.0#">
<!--
Generally, we want to move away from initial/default values being
stored in the model directly. But until we are using CellML 1.1
it is probably quite useful to include the values in the model.
-->
<!-- Global units -->
<units name="ms">
<unit prefix="milli" units="second"/>
</units>
<units name="pms">
<unit exponent="-1" prefix="milli" units="second"/>
</units>
<units name="nmol">
<unit prefix="nano" units="mole"/>
</units>
<units name="mM">
<unit units="nmol"/>
<unit exponent="-3" prefix="milli" units="metre"/>
</units>
<units name="pmspmM">
<unit units="pms"/>
<unit exponent="-1" units="mM"/>
</units>
<units name="kPa">
<unit prefix="kilo" units="pascal"/>
</units>
<component cmeta:id="interface" name="interface">
<!-- Variables we expect to be set/controlled externally -->
<variable name="time" private_interface="out" units="ms"/>
<variable initial_value="1" name="lambda" private_interface="out" units="dimensionless"/>
<variable initial_value="1" name="Ca_max" private_interface="out" units="mM"/>
<variable initial_value="1.45" name="beta" private_interface="out" units="dimensionless"/>
<variable initial_value="0.5" name="c50" private_interface="out" units="mM"/>
<variable initial_value="3" name="h" private_interface="out" units="dimensionless"/>
<variable initial_value="100" name="T_ref" private_interface="out" units="kPa"/>
<!-- Variables we want to make available externally -->
<variable name="T" private_interface="in" public_interface="out" units="kPa"/>
<variable initial_value="6.50000050729997" name="Ca_actn" private_interface="out" public_interface="out" units="mM"/>
<math xmlns="http://www.w3.org/1998/Math/MathML">
<apply id="dummy_ode_eq">
<eq/>
<apply>
<diff/>
<bvar>
<ci>time</ci>
</bvar>
<ci>Ca_actn</ci>
</apply>
<apply>
<times/>
<ci>time</ci>
<ci>Ca_max</ci>
</apply>
</apply>
</math>
<!-- Ca_actn ={Ca_actn_calculation} sel
case time <= 5.0{ms}:
time*Ca_max;
case time >= 2.0{ms}:
(2.0{ms}-time)*Ca_max;
otherwise:
0.0{mM};
endsel;-->
</component>
<!--interface-->
<component name="active_contraction">
<!-- Inputs -->
<variable name="time" public_interface="in" units="ms"/>
<variable name="lambda" public_interface="in" units="dimensionless"/>
<variable name="Ca_max" public_interface="in" units="mM"/>
<variable name="beta" public_interface="in" units="dimensionless"/>
<variable name="c50" public_interface="in" units="mM"/>
<variable name="h" public_interface="in" units="dimensionless"/>
<variable name="T_ref" public_interface="in" units="kPa"/>
<variable name="Ca_actn" public_interface="in" units="mM"/>
<!-- Outputs computed here -->
<variable name="T" public_interface="out" units="kPa"/>
<math xmlns="http://www.w3.org/1998/Math/MathML">
<apply id="T_calculation">
<eq/>
<ci>T</ci>
<apply>
<times/>
<apply>
<divide/>
<apply>
<times/>
<ci>Ca_max</ci>
<apply>
<power/>
<ci>Ca_actn</ci>
<ci>h</ci>
</apply>
</apply>
<apply>
<plus/>
<apply>
<power/>
<ci>Ca_actn</ci>
<ci>h</ci>
</apply>
<apply>
<power/>
<ci>c50</ci>
<ci>h</ci>
</apply>
</apply>
</apply>
<ci>T_ref</ci>
<apply>
<plus/>
<cn cellml:units="dimensionless">1.0</cn>
<apply>
<times/>
<ci>beta</ci>
<apply>
<minus/>
<ci>lambda</ci>
<cn cellml:units="dimensionless">1.0</cn>
</apply>
</apply>
</apply>
</apply>
</apply>
</math>
</component>
<!--active_contraction-->
<connection>
<map_components component_1="interface" component_2="active_contraction"/>
<map_variables variable_1="time" variable_2="time"/>
<map_variables variable_1="Ca_actn" variable_2="Ca_actn"/>
<map_variables variable_1="lambda" variable_2="lambda"/>
<map_variables variable_1="Ca_max" variable_2="Ca_max"/>
<map_variables variable_1="beta" variable_2="beta"/>
<map_variables variable_1="c50" variable_2="c50"/>
<map_variables variable_1="h" variable_2="h"/>
<map_variables variable_1="T_ref" variable_2="T_ref"/>
<map_variables variable_1="T" variable_2="T"/>
</connection>
<group>
<relationship_ref relationship="encapsulation"/>
<component_ref component="interface">
<component_ref component="active_contraction"/>
</component_ref>
</group>
<rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#">
<rdf:Description rdf:about="">
<creator xmlns="http://purl.org/dc/elements/1.1/">
<rdf:Description rdf:nodeID="n1"/>
</creator>
<created xmlns="http://purl.org/dc/terms/">
<rdf:Description rdf:nodeID="n2"/>
</created>
</rdf:Description>
<rdf:Description rdf:nodeID="n1">
<N xmlns="http://www.w3.org/2001/vcard-rdf/3.0#">
<rdf:Description rdf:nodeID="n3"/>
</N>
<EMAIL xmlns="http://www.w3.org/2001/vcard-rdf/3.0#">
<rdf:Description rdf:nodeID="n4"/>
</EMAIL>
<ORG xmlns="http://www.w3.org/2001/vcard-rdf/3.0#">
<rdf:Description rdf:nodeID="n5"/>
</ORG>
</rdf:Description>
<rdf:Description rdf:nodeID="n2">
<W3CDTF xml:lang="en" xmlns="http://purl.org/dc/terms/">2003-12-08</W3CDTF>
</rdf:Description>
<rdf:Description rdf:nodeID="n3">
<Family xml:lang="en" xmlns="http://www.w3.org/2001/vcard-rdf/3.0#">Nickerson</Family>
<Given xml:lang="en" xmlns="http://www.w3.org/2001/vcard-rdf/3.0#">David</Given>
</rdf:Description>
<rdf:Description rdf:nodeID="n4">
<rdf:type>
<rdf:Description rdf:about="http://imc.org/vCard/3.0#internet"/>
</rdf:type>
<rdf:value xml:lang="en">d.nickerson@auckland.ac.nz</rdf:value>
</rdf:Description>
<rdf:Description rdf:nodeID="n5">
<Orgname xml:lang="en" xmlns="http://www.w3.org/2001/vcard-rdf/3.0#">The University of Auckland</Orgname>
<Orgunit xml:lang="en" xmlns="http://www.w3.org/2001/vcard-rdf/3.0#">The Bioengineering Institute</Orgunit>
</rdf:Description>
<rdf:Description rdf:about="#nash_1998">
<cmeta:comment>
<rdf:Description rdf:nodeID="n6"/>
</cmeta:comment>
</rdf:Description>
<rdf:Description rdf:nodeID="n6">
<rdf:value xml:lang="en">
This is a CellML version of the steady-state length-tension-calcium
relationship described by Martyn Nash in his thesis.
</rdf:value>
</rdf:Description>
<rdf:Description rdf:about="#interface">
<cmeta:comment>
<rdf:Description rdf:nodeID="n7"/>
</cmeta:comment>
</rdf:Description>
<rdf:Description rdf:nodeID="n7">
<rdf:value xml:lang="en">
We'll use this component as the "interface" to the model, all
other components are hidden via encapsulation in this component.
With this model, we expect the extension ratio to be
controlled externally for non-isometric simulations.
</rdf:value>
</rdf:Description>
<rdf:Description rdf:about="#lambda_for_cmiss_eq">
<cmeta:comment>
<rdf:Description rdf:nodeID="n8"/>
</cmeta:comment>
</rdf:Description>
<rdf:Description rdf:nodeID="n8">
<rdf:value xml:lang="en">
A dummy equation that we simply use to make grabbing the
value in CMISS much easier.
</rdf:value>
</rdf:Description>
<rdf:Description rdf:about="#dummy_ode_eq">
<cmeta:comment>
<rdf:Description rdf:nodeID="n9"/>
</cmeta:comment>
</rdf:Description>
<rdf:Description rdf:nodeID="n9">
<rdf:value xml:lang="en">
We need a dummy ODE to establish time as the bound variable to
get things to work properly with CMISS.
</rdf:value>
</rdf:Description>
<rdf:Description rdf:about="#active_contraction_eq">
<cmeta:comment>
<rdf:Description rdf:nodeID="n10"/>
</cmeta:comment>
</rdf:Description>
<rdf:Description rdf:nodeID="n10">
<rdf:value xml:lang="en">
The component which defines the kinetics of the active
tension development.
</rdf:value>
</rdf:Description>
<rdf:Description rdf:about="#T_calculation_eq">
<cmeta:comment>
<rdf:Description rdf:nodeID="n11"/>
</cmeta:comment>
</rdf:Description>
<rdf:Description rdf:nodeID="n11">
<rdf:value xml:lang="en">
The kinetics of the active tension development using the
steady-state description from the Nash model.
</rdf:value>
</rdf:Description>
<rdf:Description rdf:about="#Ca_actn_calculation_eq">
<cmeta:comment>
<rdf:Description rdf:nodeID="n12"/>
</cmeta:comment>
</rdf:Description>
<rdf:Description rdf:nodeID="n12">
<rdf:value xml:lang="en">
Here we define the calcium activation transient which simply
goes from 0 to 1 and back to 0 over a period of 2ms.
</rdf:value>
</rdf:Description>
</rdf:RDF>
</model>
