- Author:
- Shelley Fong <sfon036@UoA.auckland.ac.nz>
- Date:
- 2024-12-09 10:01:24+13:00
- Desc:
- Adding link to existing models
- Permanent Source URI:
- https://staging.physiomeproject.org/workspace/c44/rawfile/06d77e4c9801dd7a4f6d69d47c58269d6776f514/BG_ABC.cellml
<?xml version='1.0' encoding='UTF-8'?>
<model name="individual_ABC" 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="1e-6" name="q_S_i" public_interface="out" units="fmol"/>
<variable initial_value="1e-3" name="q_S_o" public_interface="out" units="fmol"/>
<variable initial_value="1e-6" name="q_E_ADP" public_interface="out" units="fmol"/>
<variable initial_value="1e-6" name="q_E_ATP" public_interface="out" units="fmol"/>
<variable initial_value="1e-4" name="q_ATP" public_interface="out" units="fmol"/>
<variable initial_value="1e-6" name="q_ADP" public_interface="out" units="fmol"/>
<variable initial_value="1e-6" name="q_Pi" public_interface="out" units="fmol"/>
<variable initial_value="1e-6" name="q_S_E_ATP" public_interface="out" units="fmol"/>
<variable initial_value="1e-6" name="q_S_E_ADP" public_interface="out" units="fmol"/>
<!-- From submodule-->
<variable name="v_ReABind" public_interface="in" units="fmol_per_sec"/>
<variable name="v_ReSBind" public_interface="in" units="fmol_per_sec"/>
<variable name="v_ReHyd" public_interface="in" units="fmol_per_sec"/>
<variable name="v_ReRel" public_interface="in" units="fmol_per_sec"/>
<math xmlns="http://www.w3.org/1998/Math/MathML">
<apply>
<eq/>
<apply>
<diff/>
<bvar>
<ci>time</ci>
</bvar>
<ci>q_S_i</ci>
</apply>
<ci>v_ReHyd</ci>
</apply>
<apply>
<eq/>
<apply>
<diff/>
<bvar>
<ci>time</ci>
</bvar>
<ci>q_S_o</ci>
</apply>
<apply>
<minus/>
<ci>v_ReSBind</ci>
</apply>
</apply>
<apply>
<eq/>
<apply>
<diff/>
<bvar>
<ci>time</ci>
</bvar>
<ci>q_E_ADP</ci>
</apply>
<apply>
<plus/>
<apply>
<minus/>
<ci>v_ReSBind</ci>
</apply>
<ci>v_ReRel</ci>
</apply>
</apply>
<apply>
<eq/>
<apply>
<diff/>
<bvar>
<ci>time</ci>
</bvar>
<ci>q_E_ATP</ci>
</apply>
<apply>
<minus/>
<ci>v_ReABind</ci>
<ci>v_ReSBind</ci>
</apply>
</apply>
<apply>
<eq/>
<apply>
<diff/>
<bvar>
<ci>time</ci>
</bvar>
<ci>q_ATP</ci>
</apply>
<apply>
<minus/>
<ci>v_ReABind</ci>
</apply>
</apply>
<apply>
<eq/>
<apply>
<diff/>
<bvar>
<ci>time</ci>
</bvar>
<ci>q_ADP</ci>
</apply>
<ci>v_ReABind</ci>
</apply>
<apply>
<eq/>
<apply>
<diff/>
<bvar>
<ci>time</ci>
</bvar>
<ci>q_Pi</ci>
</apply>
<ci>v_ReHyd</ci>
</apply>
<apply>
<eq/>
<apply>
<diff/>
<bvar>
<ci>time</ci>
</bvar>
<ci>q_S_E_ATP</ci>
</apply>
<apply>
<minus/>
<ci>v_ReSBind</ci>
<ci>v_ReHyd</ci>
</apply>
</apply>
<apply>
<eq/>
<apply>
<diff/>
<bvar>
<ci>time</ci>
</bvar>
<ci>q_S_E_ADP</ci>
</apply>
<apply>
<minus/>
<ci>v_ReHyd</ci>
<ci>v_ReRel</ci>
</apply>
</apply>
</math>
</component>
<component name="ABC_parameters">
<variable initial_value="0.509703" name="kappa_ReABind" public_interface="out" units="fmol_per_sec"/>
<variable initial_value="1.85478e-07" name="kappa_ReSBind" public_interface="out" units="fmol_per_sec"/>
<variable initial_value="185478" name="kappa_ReHyd" public_interface="out" units="fmol_per_sec"/>
<variable initial_value="48186.7" name="kappa_ReRel" public_interface="out" units="fmol_per_sec"/>
<variable initial_value="1.58747e-11" name="K_S_i" public_interface="out" units="per_fmol"/>
<variable initial_value="6.46339e+08" name="K_S_o" public_interface="out" units="per_fmol"/>
<variable initial_value="0.000905319" name="K_E_ADP" public_interface="out" units="per_fmol"/>
<variable initial_value="5.7767" name="K_E_ATP" public_interface="out" units="per_fmol"/>
<variable initial_value="1.50077e+06" name="K_ATP" public_interface="out" units="per_fmol"/>
<variable initial_value="2.35199e-10" name="K_ADP" public_interface="out" units="per_fmol"/>
<variable initial_value="6.83676e-15" name="K_Pi" public_interface="out" units="per_fmol"/>
<variable initial_value="0.141881" name="K_S_E_ATP" public_interface="out" units="per_fmol"/>
<variable initial_value="0.546122" name="K_S_E_ADP" public_interface="out" units="per_fmol"/>
</component>
<component name="ABC">
<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"/>
<!-- parameters-->
<variable name="kappa_ReABind" public_interface="in" units="fmol_per_sec"/>
<variable name="kappa_ReSBind" public_interface="in" units="fmol_per_sec"/>
<variable name="kappa_ReHyd" public_interface="in" units="fmol_per_sec"/>
<variable name="kappa_ReRel" public_interface="in" units="fmol_per_sec"/>
<variable name="K_S_i" public_interface="in" units="per_fmol"/>
<variable name="K_S_o" public_interface="in" units="per_fmol"/>
<variable name="K_E_ADP" public_interface="in" units="per_fmol"/>
<variable name="K_E_ATP" public_interface="in" units="per_fmol"/>
<variable name="K_ATP" public_interface="in" units="per_fmol"/>
<variable name="K_ADP" public_interface="in" units="per_fmol"/>
<variable name="K_Pi" public_interface="in" units="per_fmol"/>
<variable name="K_S_E_ATP" public_interface="in" units="per_fmol"/>
<variable name="K_S_E_ADP" public_interface="in" units="per_fmol"/>
<!-- Input from global environment-->
<variable name="q_S_i" public_interface="in" units="fmol"/>
<variable name="q_S_o" public_interface="in" units="fmol"/>
<variable name="q_E_ADP" public_interface="in" units="fmol"/>
<variable name="q_E_ATP" public_interface="in" units="fmol"/>
<variable name="q_ATP" public_interface="in" units="fmol"/>
<variable name="q_ADP" public_interface="in" units="fmol"/>
<variable name="q_Pi" public_interface="in" units="fmol"/>
<variable name="q_S_E_ATP" public_interface="in" units="fmol"/>
<variable name="q_S_E_ADP" public_interface="in" units="fmol"/>
<!-- Constitutive parameters-->
<variable name="mu_S_i" units="J_per_mol"/>
<variable name="mu_S_o" units="J_per_mol"/>
<variable name="mu_E_ADP" units="J_per_mol"/>
<variable name="mu_E_ATP" units="J_per_mol"/>
<variable name="mu_ATP" units="J_per_mol"/>
<variable name="mu_ADP" units="J_per_mol"/>
<variable name="mu_Pi" units="J_per_mol"/>
<variable name="mu_S_E_ATP" units="J_per_mol"/>
<variable name="mu_S_E_ADP" units="J_per_mol"/>
<variable name="v_ReABind" public_interface="out" units="fmol_per_sec"/>
<variable name="v_ReSBind" public_interface="out" units="fmol_per_sec"/>
<variable name="v_ReHyd" public_interface="out" units="fmol_per_sec"/>
<variable name="v_ReRel" public_interface="out" units="fmol_per_sec"/>
<math xmlns="http://www.w3.org/1998/Math/MathML">
<apply>
<eq/>
<ci>mu_S_i</ci>
<apply>
<times/>
<ci>R</ci>
<ci>T</ci>
<apply>
<ln/>
<apply>
<times/>
<ci>K_S_i</ci>
<ci>q_S_i</ci>
</apply>
</apply>
</apply>
</apply>
<apply>
<eq/>
<ci>mu_S_o</ci>
<apply>
<times/>
<ci>R</ci>
<ci>T</ci>
<apply>
<ln/>
<apply>
<times/>
<ci>K_S_o</ci>
<ci>q_S_o</ci>
</apply>
</apply>
</apply>
</apply>
<apply>
<eq/>
<ci>mu_E_ADP</ci>
<apply>
<times/>
<ci>R</ci>
<ci>T</ci>
<apply>
<ln/>
<apply>
<times/>
<ci>K_E_ADP</ci>
<ci>q_E_ADP</ci>
</apply>
</apply>
</apply>
</apply>
<apply>
<eq/>
<ci>mu_E_ATP</ci>
<apply>
<times/>
<ci>R</ci>
<ci>T</ci>
<apply>
<ln/>
<apply>
<times/>
<ci>K_E_ATP</ci>
<ci>q_E_ATP</ci>
</apply>
</apply>
</apply>
</apply>
<apply>
<eq/>
<ci>mu_ATP</ci>
<apply>
<times/>
<ci>R</ci>
<ci>T</ci>
<apply>
<ln/>
<apply>
<times/>
<ci>K_ATP</ci>
<ci>q_ATP</ci>
</apply>
</apply>
</apply>
</apply>
<apply>
<eq/>
<ci>mu_ADP</ci>
<apply>
<times/>
<ci>R</ci>
<ci>T</ci>
<apply>
<ln/>
<apply>
<times/>
<ci>K_ADP</ci>
<ci>q_ADP</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</ci>
</apply>
</apply>
</apply>
</apply>
<apply>
<eq/>
<ci>mu_S_E_ATP</ci>
<apply>
<times/>
<ci>R</ci>
<ci>T</ci>
<apply>
<ln/>
<apply>
<times/>
<ci>K_S_E_ATP</ci>
<ci>q_S_E_ATP</ci>
</apply>
</apply>
</apply>
</apply>
<apply>
<eq/>
<ci>mu_S_E_ADP</ci>
<apply>
<times/>
<ci>R</ci>
<ci>T</ci>
<apply>
<ln/>
<apply>
<times/>
<ci>K_S_E_ADP</ci>
<ci>q_S_E_ADP</ci>
</apply>
</apply>
</apply>
</apply>
<apply>
<eq/>
<ci>v_ReABind</ci>
<apply>
<times/>
<ci>kappa_ReABind</ci>
<apply>
<minus/>
<apply>
<exp/>
<apply>
<divide/>
<apply>
<plus/>
<ci>mu_E_ADP</ci>
<ci>mu_ATP</ci>
</apply>
<apply>
<times/>
<ci>R</ci>
<ci>T</ci>
</apply>
</apply>
</apply>
<apply>
<exp/>
<apply>
<divide/>
<apply>
<plus/>
<ci>mu_E_ATP</ci>
<ci>mu_ADP</ci>
</apply>
<apply>
<times/>
<ci>R</ci>
<ci>T</ci>
</apply>
</apply>
</apply>
</apply>
</apply>
</apply>
<apply>
<eq/>
<ci>v_ReSBind</ci>
<apply>
<times/>
<ci>kappa_ReSBind</ci>
<apply>
<minus/>
<apply>
<exp/>
<apply>
<divide/>
<apply>
<plus/>
<ci>mu_S_o</ci>
<ci>mu_E_ATP</ci>
</apply>
<apply>
<times/>
<ci>R</ci>
<ci>T</ci>
</apply>
</apply>
</apply>
<apply>
<exp/>
<apply>
<divide/>
<ci>mu_S_E_ATP</ci>
<apply>
<times/>
<ci>R</ci>
<ci>T</ci>
</apply>
</apply>
</apply>
</apply>
</apply>
</apply>
<apply>
<eq/>
<ci>v_ReHyd</ci>
<apply>
<times/>
<ci>kappa_ReHyd</ci>
<apply>
<minus/>
<apply>
<exp/>
<apply>
<divide/>
<ci>mu_S_E_ATP</ci>
<apply>
<times/>
<ci>R</ci>
<ci>T</ci>
</apply>
</apply>
</apply>
<apply>
<exp/>
<apply>
<divide/>
<apply>
<plus/>
<ci>mu_S_E_ADP</ci>
<ci>mu_Pi</ci>
</apply>
<apply>
<times/>
<ci>R</ci>
<ci>T</ci>
</apply>
</apply>
</apply>
</apply>
</apply>
</apply>
<apply>
<eq/>
<ci>v_ReRel</ci>
<apply>
<times/>
<ci>kappa_ReRel</ci>
<apply>
<minus/>
<apply>
<exp/>
<apply>
<divide/>
<ci>mu_S_E_ADP</ci>
<apply>
<times/>
<ci>R</ci>
<ci>T</ci>
</apply>
</apply>
</apply>
<apply>
<exp/>
<apply>
<divide/>
<apply>
<plus/>
<ci>mu_S_i</ci>
<ci>mu_E_ADP</ci>
</apply>
<apply>
<times/>
<ci>R</ci>
<ci>T</ci>
</apply>
</apply>
</apply>
</apply>
</apply>
</apply>
</math>
</component>
<connection>
<map_components component_1="environment" component_2="ABC"/>
<map_variables variable_1="time" variable_2="time"/>
<map_variables variable_1="q_S_i" variable_2="q_S_i"/>
<map_variables variable_1="q_S_o" variable_2="q_S_o"/>
<map_variables variable_1="q_E_ADP" variable_2="q_E_ADP"/>
<map_variables variable_1="q_E_ATP" variable_2="q_E_ATP"/>
<map_variables variable_1="q_ATP" variable_2="q_ATP"/>
<map_variables variable_1="q_ADP" variable_2="q_ADP"/>
<map_variables variable_1="q_Pi" variable_2="q_Pi"/>
<map_variables variable_1="q_S_E_ATP" variable_2="q_S_E_ATP"/>
<map_variables variable_1="q_S_E_ADP" variable_2="q_S_E_ADP"/>
<map_variables variable_1="v_ReABind" variable_2="v_ReABind"/>
<map_variables variable_1="v_ReSBind" variable_2="v_ReSBind"/>
<map_variables variable_1="v_ReHyd" variable_2="v_ReHyd"/>
<map_variables variable_1="v_ReRel" variable_2="v_ReRel"/>
</connection>
<connection>
<map_components component_1="ABC" component_2="ABC_parameters"/>
<map_variables variable_1="kappa_ReABind" variable_2="kappa_ReABind"/>
<map_variables variable_1="kappa_ReSBind" variable_2="kappa_ReSBind"/>
<map_variables variable_1="kappa_ReHyd" variable_2="kappa_ReHyd"/>
<map_variables variable_1="kappa_ReRel" variable_2="kappa_ReRel"/>
<map_variables variable_1="K_S_i" variable_2="K_S_i"/>
<map_variables variable_1="K_S_o" variable_2="K_S_o"/>
<map_variables variable_1="K_E_ADP" variable_2="K_E_ADP"/>
<map_variables variable_1="K_E_ATP" variable_2="K_E_ATP"/>
<map_variables variable_1="K_ATP" variable_2="K_ATP"/>
<map_variables variable_1="K_ADP" variable_2="K_ADP"/>
<map_variables variable_1="K_Pi" variable_2="K_Pi"/>
<map_variables variable_1="K_S_E_ATP" variable_2="K_S_E_ATP"/>
<map_variables variable_1="K_S_E_ADP" variable_2="K_S_E_ADP"/>
</connection>
<connection>
<map_components component_1="constants" component_2="ABC"/>
<map_variables variable_1="R" variable_2="R"/>
<map_variables variable_1="T" variable_2="T"/>
</connection>
</model>
