- Author:
- Shelley Fong <sfon036@UoA.auckland.ac.nz>
- Date:
- 2022-05-12 10:09:04+12:00
- Desc:
- cellml sedml files for yang version added
- Permanent Source URI:
- https://models.physiomeproject.org/workspace/818/rawfile/bb5de0201cebfb862c2cfd4d37bdbdc8986d14ed/BG_HaiMurphy_original.cellml
<?xml version='1.0' encoding='UTF-8'?>
<model name="individual_HaiMurphy" xmlns="http://www.cellml.org/cellml/1.1#" xmlns:cellml="http://www.cellml.org/cellml/1.1#" xmlns:xlink="http://www.w3.org/1999/xlink">
<import xlink:href="units_and_constants/units_BG.cellml">
<units name="mM" units_ref="mM"/>
<units name="fmol" units_ref="fmol"/>
<units name="per_fmol" units_ref="per_fmol"/>
<units name="J_per_mol" units_ref="J_per_mol"/>
<units name="fmol_per_sec" units_ref="fmol_per_sec"/>
<units name="C_per_mol" units_ref="C_per_mol"/>
<units name="J_per_C" units_ref="J_per_C"/>
<units name="microm3" units_ref="microm3"/>
<units name="fF" units_ref="fF"/>
<units name="fC" units_ref="fC"/>
<units name="fA" units_ref="fA"/>
<units name="per_second" units_ref="per_second"/>
<units name="millivolt" units_ref="millivolt"/>
<units name="per_sec" units_ref="per_sec"/>
<units name="J_per_K_per_mol" units_ref="J_per_K_per_mol"/>
<units name="fmol_per_L" units_ref="fmol_per_L"/>
<units name="fmol_per_L_per_sec" units_ref="fmol_per_L_per_sec"/>
<units name="per_sec_per_fmol_per_L" units_ref="per_sec_per_fmol_per_L"/>
<units name="uM" units_ref="uM"/>
<units name="mM_per_sec" units_ref="mM_per_sec"/>
<units name="uM_per_sec" units_ref="uM_per_sec"/>
<units name="pL" units_ref="pL"/>
<units name="m_to_u" units_ref="m_to_u"/>
</import>
<import xlink:href="units_and_constants/constants_BG.cellml">
<component component_ref="constants" name="constants"/>
</import>
<component name="environment">
<variable name="time" public_interface="out" units="second"/>
<!-- initial values-->
<variable initial_value="1" name="q_A_init" units="fmol"/>
<variable initial_value="1" name="q_M_init" units="fmol"/>
<variable initial_value="0" name="q_Mp_init" units="fmol"/>
<variable initial_value="0" name="q_AM_init" units="fmol"/>
<variable initial_value="0" name="q_AMp_init" units="fmol"/>
<variable initial_value="570" name="q_Pi_init" units="fmol"/>
<!-- Global value-->
<variable name="q_A" public_interface="out" units="fmol"/>
<variable name="q_M" public_interface="out" units="fmol"/>
<variable name="q_Mp" public_interface="out" units="fmol"/>
<variable name="q_AM" public_interface="out" units="fmol"/>
<variable name="q_AMp" public_interface="out" units="fmol"/>
<variable name="q_Pi" public_interface="out" units="fmol"/>
<!-- From submodule-->
<variable name="q_A_mHaiMurphy" public_interface="in" units="fmol"/>
<variable name="q_M_mHaiMurphy" public_interface="in" units="fmol"/>
<variable name="q_Mp_mHaiMurphy" public_interface="in" units="fmol"/>
<variable name="q_AM_mHaiMurphy" public_interface="in" units="fmol"/>
<variable name="q_AMp_mHaiMurphy" public_interface="in" units="fmol"/>
<variable name="q_Pi_mHaiMurphy" public_interface="in" units="fmol"/>
<math xmlns="http://www.w3.org/1998/Math/MathML">
<apply>
<eq/>
<ci>q_A</ci>
<apply>
<plus/>
<ci>q_A_mHaiMurphy</ci>
<ci>q_A_init</ci>
</apply>
</apply>
<apply>
<eq/>
<ci>q_M</ci>
<apply>
<plus/>
<ci>q_M_mHaiMurphy</ci>
<ci>q_M_init</ci>
</apply>
</apply>
<apply>
<eq/>
<ci>q_Mp</ci>
<apply>
<plus/>
<ci>q_Mp_mHaiMurphy</ci>
<ci>q_Mp_init</ci>
</apply>
</apply>
<apply>
<eq/>
<ci>q_AM</ci>
<apply>
<plus/>
<ci>q_AM_mHaiMurphy</ci>
<ci>q_AM_init</ci>
</apply>
</apply>
<apply>
<eq/>
<ci>q_AMp</ci>
<apply>
<plus/>
<ci>q_AMp_mHaiMurphy</ci>
<ci>q_AMp_init</ci>
</apply>
</apply>
<apply>
<eq/>
<ci>q_Pi</ci>
<apply>
<plus/>
<ci>q_Pi_mHaiMurphy</ci>
<ci>q_Pi_init</ci>
</apply>
</apply>
</math>
<!-- stress calculation: from original paper,
stress = AM + AMp -->
<variable name="stress" units="dimensionless"/>
<math xmlns="http://www.w3.org/1998/Math/MathML">
<apply>
<eq/>
<ci>stress</ci>
<apply>
<divide/>
<apply>
<plus/>
<ci>q_AM</ci>
<ci>q_AMp</ci>
</apply>
<cn cellml:units="fmol">1</cn>
</apply>
</apply>
</math>
</component>
<component name="HaiMurphy_before5s_parameters">
<variable initial_value="0.525428" name="kappa_R_12" public_interface="out" units="fmol_per_sec"/>
<variable initial_value="0.420342" name="kappa_R_34" public_interface="out" units="fmol_per_sec"/>
<variable initial_value="2.10171" name="kappa_R_56" public_interface="out" units="fmol_per_sec"/>
<variable initial_value="0.0654128" name="kappa_R_78" public_interface="out" units="fmol_per_sec"/>
<variable initial_value="0.0242694" name="K_A" public_interface="out" units="per_fmol"/>
<variable initial_value="0.0212922" name="K_M" public_interface="out" units="per_fmol"/>
<variable initial_value="0.0331345" name="K_Mp" public_interface="out" units="per_fmol"/>
<variable initial_value="0.00444405" name="K_AM" public_interface="out" units="per_fmol"/>
<variable initial_value="0.00691574" name="K_AMp" public_interface="out" units="per_fmol"/>
<variable initial_value="0.0497616" name="K_Pi" public_interface="out" units="per_fmol"/>
</component>
<component name="HaiMurphy_after5s_parameters">
<variable initial_value="0.487736" name="kappa_R_12" public_interface="out" units="fmol_per_sec"/>
<variable initial_value="0.390189" name="kappa_R_34" public_interface="out" units="fmol_per_sec"/>
<variable initial_value="1.95095" name="kappa_R_56" public_interface="out" units="fmol_per_sec"/>
<variable initial_value="0.0751105" name="kappa_R_78" public_interface="out" units="fmol_per_sec"/>
<variable initial_value="0.0237587" name="K_A" public_interface="out" units="per_fmol"/>
<variable initial_value="0.0189417" name="K_M" public_interface="out" units="per_fmol"/>
<variable initial_value="0.0364624" name="K_Mp" public_interface="out" units="per_fmol"/>
<variable initial_value="0.00387027" name="K_AM" public_interface="out" units="per_fmol"/>
<variable initial_value="0.00745018" name="K_AMp" public_interface="out" units="per_fmol"/>
<variable initial_value="0.0335752" name="K_Pi" public_interface="out" units="per_fmol"/>
</component>
<component name="HaiMurphy">
<variable name="time" public_interface="in" units="second"/>
<variable name="R" public_interface="in" units="J_per_K_per_mol"/>
<variable name="T" public_interface="in" units="kelvin"/>
<!-- 2 parameter sets, to use depending on what the time is-->
<variable name="kappa_R_12" units="fmol_per_sec"/>
<variable name="kappa_R_34" units="fmol_per_sec"/>
<variable name="kappa_R_56" units="fmol_per_sec"/>
<variable name="kappa_R_78" units="fmol_per_sec"/>
<variable name="K_A" units="per_fmol"/>
<variable name="K_M" units="per_fmol"/>
<variable name="K_Mp" units="per_fmol"/>
<variable name="K_AM" units="per_fmol"/>
<variable name="K_AMp" units="per_fmol"/>
<variable name="K_Pi" units="per_fmol"/>
<variable name="kappa_R_12_before5s" public_interface="in" units="fmol_per_sec"/>
<variable name="kappa_R_34_before5s" public_interface="in" units="fmol_per_sec"/>
<variable name="kappa_R_56_before5s" public_interface="in" units="fmol_per_sec"/>
<variable name="kappa_R_78_before5s" public_interface="in" units="fmol_per_sec"/>
<variable name="K_A_before5s" public_interface="in" units="per_fmol"/>
<variable name="K_M_before5s" public_interface="in" units="per_fmol"/>
<variable name="K_Mp_before5s" public_interface="in" units="per_fmol"/>
<variable name="K_AM_before5s" public_interface="in" units="per_fmol"/>
<variable name="K_AMp_before5s" public_interface="in" units="per_fmol"/>
<variable name="K_Pi_before5s" public_interface="in" units="per_fmol"/>
<variable name="kappa_R_12_after5s" public_interface="in" units="fmol_per_sec"/>
<variable name="kappa_R_34_after5s" public_interface="in" units="fmol_per_sec"/>
<variable name="kappa_R_56_after5s" public_interface="in" units="fmol_per_sec"/>
<variable name="kappa_R_78_after5s" public_interface="in" units="fmol_per_sec"/>
<variable name="K_A_after5s" public_interface="in" units="per_fmol"/>
<variable name="K_M_after5s" public_interface="in" units="per_fmol"/>
<variable name="K_Mp_after5s" public_interface="in" units="per_fmol"/>
<variable name="K_AM_after5s" public_interface="in" units="per_fmol"/>
<variable name="K_AMp_after5s" public_interface="in" units="per_fmol"/>
<variable name="K_Pi_after5s" public_interface="in" units="per_fmol"/>
<math xmlns="http://www.w3.org/1998/Math/MathML">
<apply>
<eq/>
<ci>kappa_R_12</ci>
<piecewise>
<piece>
<ci>kappa_R_12_before5s</ci>
<apply>
<lt/>
<ci>time</ci>
<cn cellml:units="second">5</cn>
</apply>
</piece>
<otherwise>
<ci>kappa_R_12_after5s</ci>
</otherwise>
</piecewise>
</apply>
<apply>
<eq/>
<ci>kappa_R_34</ci>
<piecewise>
<piece>
<ci>kappa_R_34_before5s</ci>
<apply>
<lt/>
<ci>time</ci>
<cn cellml:units="second">5</cn>
</apply>
</piece>
<otherwise>
<ci>kappa_R_34_after5s</ci>
</otherwise>
</piecewise>
</apply>
<apply>
<eq/>
<ci>kappa_R_56</ci>
<piecewise>
<piece>
<ci>kappa_R_56_before5s</ci>
<apply>
<lt/>
<ci>time</ci>
<cn cellml:units="second">5</cn>
</apply>
</piece>
<otherwise>
<ci>kappa_R_56_after5s</ci>
</otherwise>
</piecewise>
</apply>
<apply>
<eq/>
<ci>kappa_R_78</ci>
<piecewise>
<piece>
<ci>kappa_R_78_before5s</ci>
<apply>
<lt/>
<ci>time</ci>
<cn cellml:units="second">5</cn>
</apply>
</piece>
<otherwise>
<ci>kappa_R_78_after5s</ci>
</otherwise>
</piecewise>
</apply>
<apply>
<eq/>
<ci>K_A</ci>
<piecewise>
<piece>
<ci>K_A_before5s</ci>
<apply>
<lt/>
<ci>time</ci>
<cn cellml:units="second">5</cn>
</apply>
</piece>
<otherwise>
<ci>K_A_after5s</ci>
</otherwise>
</piecewise>
</apply>
<apply>
<eq/>
<ci>K_M</ci>
<piecewise>
<piece>
<ci>K_M_before5s</ci>
<apply>
<lt/>
<ci>time</ci>
<cn cellml:units="second">5</cn>
</apply>
</piece>
<otherwise>
<ci>K_M_after5s</ci>
</otherwise>
</piecewise>
</apply>
<apply>
<eq/>
<ci>K_Mp</ci>
<piecewise>
<piece>
<ci>K_Mp_before5s</ci>
<apply>
<lt/>
<ci>time</ci>
<cn cellml:units="second">5</cn>
</apply>
</piece>
<otherwise>
<ci>K_Mp_after5s</ci>
</otherwise>
</piecewise>
</apply>
<apply>
<eq/>
<ci>K_AM</ci>
<piecewise>
<piece>
<ci>K_AM_before5s</ci>
<apply>
<lt/>
<ci>time</ci>
<cn cellml:units="second">5</cn>
</apply>
</piece>
<otherwise>
<ci>K_AM_after5s</ci>
</otherwise>
</piecewise>
</apply>
<apply>
<eq/>
<ci>K_AMp</ci>
<piecewise>
<piece>
<ci>K_AMp_before5s</ci>
<apply>
<lt/>
<ci>time</ci>
<cn cellml:units="second">5</cn>
</apply>
</piece>
<otherwise>
<ci>K_AMp_after5s</ci>
</otherwise>
</piecewise>
</apply>
<apply>
<eq/>
<ci>K_Pi</ci>
<piecewise>
<piece>
<ci>K_Pi_before5s</ci>
<apply>
<lt/>
<ci>time</ci>
<cn cellml:units="second">5</cn>
</apply>
</piece>
<otherwise>
<ci>K_Pi_after5s</ci>
</otherwise>
</piecewise>
</apply>
</math>
<!-- Input from global environment-->
<variable name="q_A_global" public_interface="in" units="fmol"/>
<variable name="q_M_global" public_interface="in" units="fmol"/>
<variable name="q_Mp_global" public_interface="in" units="fmol"/>
<variable name="q_AM_global" public_interface="in" units="fmol"/>
<variable name="q_AMp_global" public_interface="in" units="fmol"/>
<variable name="q_Pi_global" public_interface="in" units="fmol"/>
<!-- Output to global environment-->
<variable initial_value="1e-16" name="q_A" public_interface="out" units="fmol"/>
<variable initial_value="1e-16" name="q_M" public_interface="out" units="fmol"/>
<variable initial_value="1e-16" name="q_Mp" public_interface="out" units="fmol"/>
<variable initial_value="1e-16" name="q_AM" public_interface="out" units="fmol"/>
<variable initial_value="1e-16" name="q_AMp" public_interface="out" units="fmol"/>
<variable initial_value="1e-16" name="q_Pi" public_interface="out" units="fmol"/>
<!-- Constitutive parameters-->
<variable name="mu_A" units="J_per_mol"/>
<variable name="mu_M" units="J_per_mol"/>
<variable name="mu_Mp" units="J_per_mol"/>
<variable name="mu_AM" units="J_per_mol"/>
<variable name="mu_AMp" units="J_per_mol"/>
<variable name="mu_Pi" units="J_per_mol"/>
<variable name="v_R_12" units="fmol_per_sec"/>
<variable name="v_R_34" units="fmol_per_sec"/>
<variable name="v_R_56" units="fmol_per_sec"/>
<variable name="v_R_78" units="fmol_per_sec"/>
<math xmlns="http://www.w3.org/1998/Math/MathML">
<apply>
<eq/>
<ci>mu_A</ci>
<apply>
<times/>
<ci>R</ci>
<ci>T</ci>
<apply>
<ln/>
<apply>
<times/>
<ci>K_A</ci>
<ci>q_A_global</ci>
</apply>
</apply>
</apply>
</apply>
<apply>
<eq/>
<ci>mu_M</ci>
<apply>
<times/>
<ci>R</ci>
<ci>T</ci>
<apply>
<ln/>
<apply>
<times/>
<ci>K_M</ci>
<ci>q_M_global</ci>
</apply>
</apply>
</apply>
</apply>
<apply>
<eq/>
<ci>mu_Mp</ci>
<apply>
<times/>
<ci>R</ci>
<ci>T</ci>
<apply>
<ln/>
<apply>
<times/>
<ci>K_Mp</ci>
<ci>q_Mp_global</ci>
</apply>
</apply>
</apply>
</apply>
<apply>
<eq/>
<ci>mu_AM</ci>
<apply>
<times/>
<ci>R</ci>
<ci>T</ci>
<apply>
<ln/>
<apply>
<times/>
<ci>K_AM</ci>
<ci>q_AM_global</ci>
</apply>
</apply>
</apply>
</apply>
<apply>
<eq/>
<ci>mu_AMp</ci>
<apply>
<times/>
<ci>R</ci>
<ci>T</ci>
<apply>
<ln/>
<apply>
<times/>
<ci>K_AMp</ci>
<ci>q_AMp_global</ci>
</apply>
</apply>
</apply>
</apply>
<apply>
<eq/>
<ci>mu_Pi</ci>
<apply>
<times/>
<ci>R</ci>
<ci>T</ci>
<apply>
<ln/>
<apply>
<times/>
<ci>K_Pi</ci>
<ci>q_Pi_global</ci>
</apply>
</apply>
</apply>
</apply>
<apply>
<eq/>
<ci>v_R_12</ci>
<apply>
<times/>
<ci>kappa_R_12</ci>
<apply>
<minus/>
<apply>
<exp/>
<apply>
<divide/>
<apply>
<plus/>
<ci>mu_M</ci>
<ci>mu_Pi</ci>
</apply>
<apply>
<times/>
<ci>R</ci>
<ci>T</ci>
</apply>
</apply>
</apply>
<apply>
<exp/>
<apply>
<divide/>
<ci>mu_Mp</ci>
<apply>
<times/>
<ci>R</ci>
<ci>T</ci>
</apply>
</apply>
</apply>
</apply>
</apply>
</apply>
<apply>
<eq/>
<ci>v_R_34</ci>
<apply>
<times/>
<ci>kappa_R_34</ci>
<apply>
<minus/>
<apply>
<exp/>
<apply>
<divide/>
<apply>
<plus/>
<ci>mu_A</ci>
<ci>mu_Mp</ci>
</apply>
<apply>
<times/>
<ci>R</ci>
<ci>T</ci>
</apply>
</apply>
</apply>
<apply>
<exp/>
<apply>
<divide/>
<ci>mu_AMp</ci>
<apply>
<times/>
<ci>R</ci>
<ci>T</ci>
</apply>
</apply>
</apply>
</apply>
</apply>
</apply>
<apply>
<eq/>
<ci>v_R_56</ci>
<apply>
<times/>
<ci>kappa_R_56</ci>
<apply>
<minus/>
<apply>
<exp/>
<apply>
<divide/>
<ci>mu_AMp</ci>
<apply>
<times/>
<ci>R</ci>
<ci>T</ci>
</apply>
</apply>
</apply>
<apply>
<exp/>
<apply>
<divide/>
<apply>
<plus/>
<ci>mu_AM</ci>
<ci>mu_Pi</ci>
</apply>
<apply>
<times/>
<ci>R</ci>
<ci>T</ci>
</apply>
</apply>
</apply>
</apply>
</apply>
</apply>
<apply>
<eq/>
<ci>v_R_78</ci>
<apply>
<times/>
<ci>kappa_R_78</ci>
<apply>
<minus/>
<apply>
<exp/>
<apply>
<divide/>
<ci>mu_AM</ci>
<apply>
<times/>
<ci>R</ci>
<ci>T</ci>
</apply>
</apply>
</apply>
<apply>
<exp/>
<apply>
<divide/>
<apply>
<plus/>
<ci>mu_A</ci>
<ci>mu_M</ci>
</apply>
<apply>
<times/>
<ci>R</ci>
<ci>T</ci>
</apply>
</apply>
</apply>
</apply>
</apply>
</apply>
<apply>
<eq/>
<apply>
<diff/>
<bvar>
<ci>time</ci>
</bvar>
<ci>q_A</ci>
</apply>
<apply>
<plus/>
<apply>
<minus/>
<ci>v_R_34</ci>
</apply>
<ci>v_R_78</ci>
</apply>
</apply>
<apply>
<eq/>
<apply>
<diff/>
<bvar>
<ci>time</ci>
</bvar>
<ci>q_M</ci>
</apply>
<apply>
<plus/>
<apply>
<minus/>
<ci>v_R_12</ci>
</apply>
<ci>v_R_78</ci>
</apply>
</apply>
<apply>
<eq/>
<apply>
<diff/>
<bvar>
<ci>time</ci>
</bvar>
<ci>q_Mp</ci>
</apply>
<apply>
<minus/>
<ci>v_R_12</ci>
<ci>v_R_34</ci>
</apply>
</apply>
<apply>
<eq/>
<apply>
<diff/>
<bvar>
<ci>time</ci>
</bvar>
<ci>q_AM</ci>
</apply>
<apply>
<minus/>
<ci>v_R_56</ci>
<ci>v_R_78</ci>
</apply>
</apply>
<apply>
<eq/>
<apply>
<diff/>
<bvar>
<ci>time</ci>
</bvar>
<ci>q_AMp</ci>
</apply>
<apply>
<minus/>
<ci>v_R_34</ci>
<ci>v_R_56</ci>
</apply>
</apply>
<apply>
<eq/>
<apply>
<diff/>
<bvar>
<ci>time</ci>
</bvar>
<ci>q_Pi</ci>
</apply>
<apply>
<plus/>
<apply>
<minus/>
<ci>v_R_12</ci>
</apply>
<ci>v_R_56</ci>
</apply>
</apply>
</math>
</component>
<connection>
<map_components component_1="environment" component_2="HaiMurphy"/>
<map_variables variable_1="time" variable_2="time"/>
<map_variables variable_1="q_A_mHaiMurphy" variable_2="q_A"/>
<map_variables variable_1="q_A" variable_2="q_A_global"/>
<map_variables variable_1="q_M_mHaiMurphy" variable_2="q_M"/>
<map_variables variable_1="q_M" variable_2="q_M_global"/>
<map_variables variable_1="q_Mp_mHaiMurphy" variable_2="q_Mp"/>
<map_variables variable_1="q_Mp" variable_2="q_Mp_global"/>
<map_variables variable_1="q_AM_mHaiMurphy" variable_2="q_AM"/>
<map_variables variable_1="q_AM" variable_2="q_AM_global"/>
<map_variables variable_1="q_AMp_mHaiMurphy" variable_2="q_AMp"/>
<map_variables variable_1="q_AMp" variable_2="q_AMp_global"/>
<map_variables variable_1="q_Pi_mHaiMurphy" variable_2="q_Pi"/>
<map_variables variable_1="q_Pi" variable_2="q_Pi_global"/>
</connection>
<connection>
<map_components component_1="HaiMurphy" component_2="HaiMurphy_before5s_parameters"/>
<map_variables variable_1="kappa_R_12_before5s" variable_2="kappa_R_12"/>
<map_variables variable_1="kappa_R_34_before5s" variable_2="kappa_R_34"/>
<map_variables variable_1="kappa_R_56_before5s" variable_2="kappa_R_56"/>
<map_variables variable_1="kappa_R_78_before5s" variable_2="kappa_R_78"/>
<map_variables variable_1="K_A_before5s" variable_2="K_A"/>
<map_variables variable_1="K_M_before5s" variable_2="K_M"/>
<map_variables variable_1="K_Mp_before5s" variable_2="K_Mp"/>
<map_variables variable_1="K_AM_before5s" variable_2="K_AM"/>
<map_variables variable_1="K_AMp_before5s" variable_2="K_AMp"/>
<map_variables variable_1="K_Pi_before5s" variable_2="K_Pi"/>
</connection>
<connection>
<map_components component_1="HaiMurphy" component_2="HaiMurphy_after5s_parameters"/>
<map_variables variable_1="kappa_R_12_after5s" variable_2="kappa_R_12"/>
<map_variables variable_1="kappa_R_34_after5s" variable_2="kappa_R_34"/>
<map_variables variable_1="kappa_R_56_after5s" variable_2="kappa_R_56"/>
<map_variables variable_1="kappa_R_78_after5s" variable_2="kappa_R_78"/>
<map_variables variable_1="K_A_after5s" variable_2="K_A"/>
<map_variables variable_1="K_M_after5s" variable_2="K_M"/>
<map_variables variable_1="K_Mp_after5s" variable_2="K_Mp"/>
<map_variables variable_1="K_AM_after5s" variable_2="K_AM"/>
<map_variables variable_1="K_AMp_after5s" variable_2="K_AMp"/>
<map_variables variable_1="K_Pi_after5s" variable_2="K_Pi"/>
</connection>
<connection>
<map_components component_1="constants" component_2="HaiMurphy"/>
<map_variables variable_1="R" variable_2="R"/>
<map_variables variable_1="T" variable_2="T"/>
</connection>
</model>
