- Author:
- Randall Britten <r.britten@auckland.ac.nz>
- Date:
- 2014-03-10 12:37:50+13:00
- Desc:
- Snapshot of partial progress towards a CellML representation, based on the BM file.
At this stage, this aimed just at the Respiration component, and without physical units, or any work to validate that the simulation results are correct.
A more detailed version history to this point is available at https://github.com/codecurve/Ikeda-et-al-1979
- Permanent Source URI:
- http://models.cellml.org/workspace/193/rawfile/e837300b086b879f3016fa777f83b9199afd1ee8/cellml/Respiration.cellml
<?xml version="1.0"?>
<model xmlns="http://www.cellml.org/cellml/1.1#" name="Ikeda_Respiration">
<component name="Main">
<math xmlns="http://www.w3.org/1998/Math/MathML">
<apply id="1">
<eq/>
<ci>XHB
</ci>
<cn xmlns:cellml="http://www.cellml.org/cellml/1.1#" cellml:units="dimensionless">15
</cn>
</apply>
<apply id="2">
<eq/>
<ci>PBA
</ci>
<cn xmlns:cellml="http://www.cellml.org/cellml/1.1#" cellml:units="dimensionless">760
</cn>
</apply>
<apply id="3">
<eq/>
<ci>PBL
</ci>
<apply>
<minus/>
<ci>PBA
</ci>
<cn xmlns:cellml="http://www.cellml.org/cellml/1.1#" cellml:units="dimensionless">47
</cn>
</apply>
</apply>
<apply id="4">
<eq/>
<ci>VAL
</ci>
<cn xmlns:cellml="http://www.cellml.org/cellml/1.1#" cellml:units="dimensionless">3
</cn>
</apply>
<apply id="5">
<eq/>
<ci>MRCO
</ci>
<cn xmlns:cellml="http://www.cellml.org/cellml/1.1#" cellml:units="dimensionless">0.2318
</cn>
</apply>
<apply id="6">
<eq/>
<ci>MRO2
</ci>
<cn xmlns:cellml="http://www.cellml.org/cellml/1.1#" cellml:units="dimensionless">0.2591
</cn>
</apply>
<apply id="7">
<eq/>
<apply>
<diff/>
<bvar>
<ci>t
</ci>
</bvar>
<ci>FCOA
</ci>
</apply>
<apply>
<divide/>
<apply>
<plus/>
<apply>
<times/>
<ci>VI
</ci>
<apply>
<minus/>
<ci>FCOI
</ci>
<ci>FCOA
</ci>
</apply>
</apply>
<apply>
<times/>
<apply>
<divide/>
<cn xmlns:cellml="http://www.cellml.org/cellml/1.1#" cellml:units="dimensionless">863
</cn>
<apply>
<minus/>
<ci>PBA
</ci>
<cn xmlns:cellml="http://www.cellml.org/cellml/1.1#" cellml:units="dimensionless">47
</cn>
</apply>
</apply>
<ci>QCO
</ci>
<apply>
<minus/>
<ci>UCOV
</ci>
<ci>UCOA
</ci>
</apply>
</apply>
</apply>
<ci>VAL
</ci>
</apply>
</apply>
<apply id="8">
<eq/>
<apply>
<diff/>
<bvar>
<ci>t
</ci>
</bvar>
<ci>FO2A
</ci>
</apply>
<apply>
<divide/>
<apply>
<plus/>
<apply>
<times/>
<ci>VI
</ci>
<apply>
<minus/>
<ci>FO2I
</ci>
<ci>FO2A
</ci>
</apply>
</apply>
<apply>
<times/>
<apply>
<divide/>
<cn xmlns:cellml="http://www.cellml.org/cellml/1.1#" cellml:units="dimensionless">863
</cn>
<apply>
<minus/>
<ci>PBA
</ci>
<cn xmlns:cellml="http://www.cellml.org/cellml/1.1#" cellml:units="dimensionless">47
</cn>
</apply>
</apply>
<ci>QCO
</ci>
<apply>
<minus/>
<ci>UO2V
</ci>
<ci>UO2A
</ci>
</apply>
</apply>
</apply>
<ci>VAL
</ci>
</apply>
</apply>
<apply id="9">
<eq/>
<apply>
<diff/>
<bvar>
<ci>t
</ci>
</bvar>
<ci>UCOV
</ci>
</apply>
<apply>
<divide/>
<apply>
<plus/>
<ci>MRCO
</ci>
<apply>
<times/>
<ci>QCO
</ci>
<apply>
<minus/>
<ci>UCOA
</ci>
<ci>UCOV
</ci>
</apply>
</apply>
</apply>
<ci>VTW
</ci>
</apply>
</apply>
<apply id="10">
<eq/>
<apply>
<diff/>
<bvar>
<ci>t
</ci>
</bvar>
<ci>UO2V
</ci>
</apply>
<apply>
<divide/>
<apply>
<plus/>
<apply>
<minus/>
<ci>MRO2
</ci>
</apply>
<apply>
<times/>
<ci>QCO
</ci>
<apply>
<minus/>
<ci>UO2A
</ci>
<ci>UO2V
</ci>
</apply>
</apply>
</apply>
<ci>VTW
</ci>
</apply>
</apply>
<apply id="11">
<eq/>
<ci>UCOA
</ci>
<apply>
<plus/>
<apply>
<times/>
<cn xmlns:cellml="http://www.cellml.org/cellml/1.1#" cellml:units="dimensionless">0.0006732
</cn>
<ci>PCOA
</ci>
</apply>
<apply>
<times/>
<cn xmlns:cellml="http://www.cellml.org/cellml/1.1#" cellml:units="dimensionless">0.02226
</cn>
<ci>XCO3
</ci>
</apply>
</apply>
</apply>
<apply id="12">
<eq/>
<ci>UO2A
</ci>
<apply>
<plus/>
<apply>
<times/>
<cn xmlns:cellml="http://www.cellml.org/cellml/1.1#" cellml:units="dimensionless">0.00003168
</cn>
<ci>PO2A
</ci>
</apply>
<ci>UHBO
</ci>
</apply>
</apply>
<apply id="13">
<eq/>
<apply>
<diff/>
<bvar>
<ci>t
</ci>
</bvar>
<ci>VI
</ci>
</apply>
<apply>
<divide/>
<apply>
<minus/>
<apply>
<times/>
<ci>VR
</ci>
<ci>VI0
</ci>
</apply>
<ci>VI
</ci>
</apply>
<ci>TRSP1
</ci>
</apply>
</apply>
<apply id="14">
<eq/>
<ci>k1
</ci>
<piecewise>
<piece>
<cn xmlns:cellml="http://www.cellml.org/cellml/1.1#" cellml:units="dimensionless">0.22
</cn>
<apply>
<leq/>
<ci>PHA
</ci>
<cn xmlns:cellml="http://www.cellml.org/cellml/1.1#" cellml:units="dimensionless">7.4
</cn>
</apply>
</piece>
<otherwise>
<cn xmlns:cellml="http://www.cellml.org/cellml/1.1#" cellml:units="dimensionless">0.0258
</cn>
</otherwise>
</piecewise>
</apply>
<apply id="15">
<eq/>
<ci>k6
</ci>
<piecewise>
<piece>
<apply>
<minus/>
<cn xmlns:cellml="http://www.cellml.org/cellml/1.1#" cellml:units="dimensionless">12.734
</cn>
</apply>
<apply>
<leq/>
<ci>PHA
</ci>
<cn xmlns:cellml="http://www.cellml.org/cellml/1.1#" cellml:units="dimensionless">7.4
</cn>
</apply>
</piece>
<otherwise>
<apply>
<minus/>
<cn xmlns:cellml="http://www.cellml.org/cellml/1.1#" cellml:units="dimensionless">5.003
</cn>
</apply>
</otherwise>
</piecewise>
</apply>
<apply id="16">
<eq/>
<ci>k3
</ci>
<cn xmlns:cellml="http://www.cellml.org/cellml/1.1#" cellml:units="dimensionless">0.58
</cn>
</apply>
<apply id="17">
<eq/>
<ci>k4
</ci>
<cn xmlns:cellml="http://www.cellml.org/cellml/1.1#" cellml:units="dimensionless">3.496
</cn>
</apply>
<apply id="18">
<eq/>
<ci>k2
</ci>
<piecewise>
<piece>
<cn xmlns:cellml="http://www.cellml.org/cellml/1.1#" cellml:units="dimensionless">1
</cn>
<apply>
<gt/>
<ci>PCOA
</ci>
<cn xmlns:cellml="http://www.cellml.org/cellml/1.1#" cellml:units="dimensionless">40
</cn>
</apply>
</piece>
<otherwise>
<cn xmlns:cellml="http://www.cellml.org/cellml/1.1#" cellml:units="dimensionless">0.0396
</cn>
</otherwise>
</piecewise>
</apply>
<apply id="19">
<eq/>
<ci>k5
</ci>
<piecewise>
<piece>
<apply>
<minus/>
<cn xmlns:cellml="http://www.cellml.org/cellml/1.1#" cellml:units="dimensionless">32.079999999999998
</cn>
</apply>
<apply>
<gt/>
<ci>PCOA
</ci>
<cn xmlns:cellml="http://www.cellml.org/cellml/1.1#" cellml:units="dimensionless">40
</cn>
</apply>
</piece>
<otherwise>
<cn xmlns:cellml="http://www.cellml.org/cellml/1.1#" cellml:units="dimensionless">160.110000000000014
</cn>
</otherwise>
</piecewise>
</apply>
<apply id="20">
<eq/>
<ci>VR
</ci>
<apply>
<max/>
<apply>
<plus/>
<apply>
<times/>
<ci>k1
</ci>
<ci>H
</ci>
</apply>
<apply>
<times/>
<ci>k2
</ci>
<apply>
<plus/>
<ci>k3
</ci>
<apply>
<divide/>
<ci>k4
</ci>
<apply>
<minus/>
<ci>PO2A
</ci>
<cn xmlns:cellml="http://www.cellml.org/cellml/1.1#" cellml:units="dimensionless">32
</cn>
</apply>
</apply>
</apply>
<apply>
<plus/>
<ci>PCOA
</ci>
<ci>k5
</ci>
</apply>
</apply>
<ci>k6
</ci>
</apply>
<cn xmlns:cellml="http://www.cellml.org/cellml/1.1#" cellml:units="dimensionless">0
</cn>
</apply>
</apply>
<apply id="21">
<eq/>
<ci>VI0
</ci>
<cn xmlns:cellml="http://www.cellml.org/cellml/1.1#" cellml:units="dimensionless">5
</cn>
</apply>
<apply id="22">
<eq/>
<ci>H
</ci>
<apply>
<power/>
<cn xmlns:cellml="http://www.cellml.org/cellml/1.1#" cellml:units="dimensionless">10
</cn>
<apply>
<minus/>
<cn xmlns:cellml="http://www.cellml.org/cellml/1.1#" cellml:units="dimensionless">9
</cn>
<ci>PHA
</ci>
</apply>
</apply>
</apply>
<apply id="23">
<eq/>
<ci>f
</ci>
<apply>
<power/>
<apply>
<minus/>
<cn xmlns:cellml="http://www.cellml.org/cellml/1.1#" cellml:units="dimensionless">1
</cn>
<apply>
<exp/>
<apply>
<times/>
<apply>
<minus/>
<ci>PO2A
</ci>
</apply>
<ci>g
</ci>
</apply>
</apply>
</apply>
<cn xmlns:cellml="http://www.cellml.org/cellml/1.1#" cellml:units="dimensionless">2
</cn>
</apply>
</apply>
<apply id="24">
<eq/>
<ci>g
</ci>
<apply>
<minus/>
<apply>
<plus/>
<apply>
<minus/>
<apply>
<times/>
<cn xmlns:cellml="http://www.cellml.org/cellml/1.1#" cellml:units="dimensionless">0.0066815
</cn>
<apply>
<power/>
<ci>PHA
</ci>
<cn xmlns:cellml="http://www.cellml.org/cellml/1.1#" cellml:units="dimensionless">3
</cn>
</apply>
</apply>
<apply>
<times/>
<cn xmlns:cellml="http://www.cellml.org/cellml/1.1#" cellml:units="dimensionless">0.10098
</cn>
<apply>
<power/>
<ci>PHA
</ci>
<cn xmlns:cellml="http://www.cellml.org/cellml/1.1#" cellml:units="dimensionless">2
</cn>
</apply>
</apply>
</apply>
<apply>
<times/>
<cn xmlns:cellml="http://www.cellml.org/cellml/1.1#" cellml:units="dimensionless">0.44921
</cn>
<ci>PHA
</ci>
</apply>
</apply>
<cn xmlns:cellml="http://www.cellml.org/cellml/1.1#" cellml:units="dimensionless">0.454
</cn>
</apply>
</apply>
<apply id="25">
<eq/>
<ci>UHBO
</ci>
<apply>
<times/>
<ci>UHB
</ci>
<ci>f
</ci>
</apply>
</apply>
<apply id="26">
<eq/>
<ci>DCLA
</ci>
<apply>
<minus/>
<ci>XCO3
</ci>
<ci>STBC
</ci>
</apply>
</apply>
<apply id="27">
<eq/>
<ci>UHB
</ci>
<apply>
<divide/>
<ci>XHB
</ci>
<cn xmlns:cellml="http://www.cellml.org/cellml/1.1#" cellml:units="dimensionless">75
</cn>
</apply>
</apply>
<apply id="28">
<eq/>
<ci>PCOA
</ci>
<apply>
<times/>
<ci>FCOA
</ci>
<apply>
<minus/>
<ci>PBA
</ci>
<cn xmlns:cellml="http://www.cellml.org/cellml/1.1#" cellml:units="dimensionless">47
</cn>
</apply>
</apply>
</apply>
<apply id="29">
<eq/>
<ci>PO2A
</ci>
<apply>
<times/>
<ci>FO2A
</ci>
<apply>
<minus/>
<ci>PBA
</ci>
<cn xmlns:cellml="http://www.cellml.org/cellml/1.1#" cellml:units="dimensionless">47
</cn>
</apply>
</apply>
</apply>
<apply id="30">
<eq/>
<ci>PHA
</ci>
<apply>
<plus/>
<cn xmlns:cellml="http://www.cellml.org/cellml/1.1#" cellml:units="dimensionless">6.1
</cn>
<apply>
<log/>
<apply>
<divide/>
<ci>XCO3
</ci>
<apply>
<times/>
<cn xmlns:cellml="http://www.cellml.org/cellml/1.1#" cellml:units="dimensionless">0.03
</cn>
<ci>PCOA
</ci>
</apply>
</apply>
</apply>
</apply>
</apply>
<apply id="31">
<eq/>
<ci>XCO0
</ci>
<apply>
<plus/>
<apply>
<minus/>
<ci>STBC
</ci>
<apply>
<times/>
<apply>
<plus/>
<apply>
<times/>
<cn xmlns:cellml="http://www.cellml.org/cellml/1.1#" cellml:units="dimensionless">0.527
</cn>
<ci>XHB
</ci>
</apply>
<cn xmlns:cellml="http://www.cellml.org/cellml/1.1#" cellml:units="dimensionless">3.7
</cn>
</apply>
<apply>
<minus/>
<ci>PHA
</ci>
<cn xmlns:cellml="http://www.cellml.org/cellml/1.1#" cellml:units="dimensionless">7.4
</cn>
</apply>
</apply>
</apply>
<apply>
<divide/>
<apply>
<times/>
<cn xmlns:cellml="http://www.cellml.org/cellml/1.1#" cellml:units="dimensionless">0.375
</cn>
<apply>
<minus/>
<ci>UHB
</ci>
<ci>UHBO
</ci>
</apply>
</apply>
<cn xmlns:cellml="http://www.cellml.org/cellml/1.1#" cellml:units="dimensionless">0.02226
</cn>
</apply>
</apply>
</apply>
<apply id="32">
<eq/>
<apply>
<diff/>
<bvar>
<ci>t
</ci>
</bvar>
<ci>XCO3
</ci>
</apply>
<apply>
<divide/>
<apply>
<minus/>
<ci>XCO0
</ci>
<ci>XCO3
</ci>
</apply>
<ci>TRSP
</ci>
</apply>
</apply>
</math>
<variable name="XHB" units="dimensionless"/>
<variable name="PBA" units="dimensionless"/>
<variable name="PBL" units="dimensionless"/>
<variable name="VAL" units="dimensionless"/>
<variable name="MRCO" units="dimensionless"/>
<variable name="MRO2" units="dimensionless"/>
<variable name="t" units="dimensionless"/>
<variable initial_value="0.0561" name="FCOA" units="dimensionless"/>
<variable initial_value="0.1473" name="FO2A" units="dimensionless"/>
<variable initial_value="5" name="VI" units="dimensionless"/>
<variable name="FCOI" units="dimensionless"/>
<variable name="FO2I" units="dimensionless"/>
<variable initial_value="0.6075" name="UCOV" units="dimensionless"/>
<variable name="QCO" public_interface="in" units="dimensionless"/>
<variable name="UCOA" units="dimensionless"/>
<variable name="VTW" public_interface="in" units="dimensionless"/>
<variable initial_value="0.1515" name="UO2V" units="dimensionless"/>
<variable name="UO2A" units="dimensionless"/>
<variable name="VR" units="dimensionless"/>
<variable name="VI0" units="dimensionless"/>
<variable name="TRSP1" public_interface="in" units="dimensionless"/>
<variable name="k1" units="dimensionless"/>
<variable name="PHA" units="dimensionless"/>
<variable name="k6" units="dimensionless"/>
<variable name="k3" units="dimensionless"/>
<variable name="k4" units="dimensionless"/>
<variable name="k2" units="dimensionless"/>
<variable name="PCOA" units="dimensionless"/>
<variable name="H" units="dimensionless"/>
<variable name="PO2A" units="dimensionless"/>
<variable name="f" units="dimensionless"/>
<variable name="UHBO" units="dimensionless"/>
<variable name="UHB" units="dimensionless"/>
<variable name="g" units="dimensionless"/>
<variable name="DCLA" units="dimensionless"/>
<variable initial_value="24" name="XCO3" units="dimensionless"/>
<variable name="STBC" public_interface="in" units="dimensionless"/>
<variable name="XCO0" units="dimensionless"/>
<variable name="TRSP" public_interface="in" units="dimensionless"/>
<variable name="k5" units="dimensionless"/>
<math xmlns="http://www.w3.org/1998/Math/MathML">
<apply id="33">
<eq/>
<ci>FCOI
</ci>
<cn xmlns:cellml="http://www.cellml.org/cellml/1.1#" cellml:units="dimensionless">0
</cn>
</apply>
<apply id="34">
<eq/>
<ci>FO2I
</ci>
<cn xmlns:cellml="http://www.cellml.org/cellml/1.1#" cellml:units="dimensionless">0.21
</cn>
</apply>
</math>
</component>
<component name="InputsDummies">
<math xmlns="http://www.w3.org/1998/Math/MathML">
<apply id="35">
<eq/>
<ci>STBC
</ci>
<cn xmlns:cellml="http://www.cellml.org/cellml/1.1#" cellml:units="dimensionless">24
</cn>
</apply>
<apply id="36">
<eq/>
<ci>QCO
</ci>
<cn xmlns:cellml="http://www.cellml.org/cellml/1.1#" cellml:units="dimensionless">5
</cn>
</apply>
<apply id="37">
<eq/>
<ci>VTW
</ci>
<cn xmlns:cellml="http://www.cellml.org/cellml/1.1#" cellml:units="dimensionless">31
</cn>
</apply>
<apply id="38">
<eq/>
<ci>TRSP
</ci>
<cn xmlns:cellml="http://www.cellml.org/cellml/1.1#" cellml:units="dimensionless">1
</cn>
</apply>
<apply id="39">
<eq/>
<ci>TRSP1
</ci>
<cn xmlns:cellml="http://www.cellml.org/cellml/1.1#" cellml:units="dimensionless">2
</cn>
</apply>
</math>
<variable name="STBC" public_interface="out" units="dimensionless"/>
<variable name="QCO" public_interface="out" units="dimensionless"/>
<variable name="VTW" public_interface="out" units="dimensionless"/>
<variable name="TRSP1" public_interface="out" units="dimensionless"/>
<variable name="TRSP" public_interface="out" units="dimensionless"/>
</component>
<connection>
<map_components component_1="Main" component_2="InputsDummies"/>
<map_variables variable_1="STBC" variable_2="STBC"/>
<map_variables variable_1="QCO" variable_2="QCO"/>
<map_variables variable_1="VTW" variable_2="VTW"/>
<map_variables variable_1="TRSP" variable_2="TRSP"/>
<map_variables variable_1="TRSP1" variable_2="TRSP1"/>
</connection>
</model>
