- Author:
- Shelley Fong <sfon036@UoA.auckland.ac.nz>
- Date:
- 2022-05-13 11:56:11+12:00
- Desc:
- Fixing equations
- Permanent Source URI:
- https://models.physiomeproject.org/workspace/857/rawfile/764c22a661800aa2d3173388426c3b88d31ebc80/BG_sGC.cellml
<?xml version='1.0' encoding='UTF-8'?>
<model name="individual_sGC" 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="J_per_K_per_mol" units_ref="J_per_K_per_mol"/>
<units name="mM_per_sec" units_ref="mM_per_sec"/>
<units name="pL" units_ref="pL"/>
<units name="C_per_mol" units_ref="C_per_mol"/>
</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-18" name="q_Eb" public_interface="out" units="fmol"/>
<variable initial_value="0.00836" name="q_NO" public_interface="out" units="fmol"/>
<variable initial_value="1e-18" name="q_E6c" public_interface="out" units="fmol"/>
<variable initial_value="1e-18" name="q_E5c" public_interface="out" units="fmol"/>
<variable initial_value="1e-18" name="q_cGMP" public_interface="out" units="fmol"/>
<variable initial_value="1e-18" name="q_NO_product" public_interface="out" units="fmol"/>
<!-- From submodule-->
<variable name="v_R_1_sGC" public_interface="in" units="fmol_per_sec"/>
<variable name="v_R_2_sGC" public_interface="in" units="fmol_per_sec"/>
<variable name="v_R_3_sGC" public_interface="in" units="fmol_per_sec"/>
<variable name="v_R_4_sGC" public_interface="in" units="fmol_per_sec"/>
<variable name="v_R_DNO_sGC" public_interface="in" units="fmol_per_sec"/>
<!-- constant rate of NO generation, converted from kinetic model J_NO-->
<variable initial_value="0.000114" name="v_NO_generation" units="fmol_per_sec"/>
<math xmlns="http://www.w3.org/1998/Math/MathML">
<apply>
<eq/>
<apply>
<diff/>
<bvar>
<ci>time</ci>
</bvar>
<ci>q_Eb</ci>
</apply>
<apply>
<plus/>
<apply>
<minus/>
<ci>v_R_1_sGC</ci>
</apply>
<ci>v_R_4_sGC</ci>
</apply>
</apply>
<apply>
<eq/>
<apply>
<diff/>
<bvar>
<ci>time</ci>
</bvar>
<ci>q_NO</ci>
</apply>
<apply>
<plus/>
<apply>
<minus/>
<apply>
<plus/>
<apply>
<minus/>
<ci>v_R_1_sGC</ci>
</apply>
<ci>v_R_4_sGC</ci>
</apply>
<ci>v_R_DNO_sGC</ci>
</apply>
<ci>v_NO_generation</ci>
</apply>
</apply>
<apply>
<eq/>
<apply>
<diff/>
<bvar>
<ci>time</ci>
</bvar>
<ci>q_E6c</ci>
</apply>
<apply>
<minus/>
<apply>
<minus/>
<ci>v_R_1_sGC</ci>
<ci>v_R_2_sGC</ci>
</apply>
<ci>v_R_3_sGC</ci>
</apply>
</apply>
<apply>
<eq/>
<apply>
<diff/>
<bvar>
<ci>time</ci>
</bvar>
<ci>q_E5c</ci>
</apply>
<apply>
<minus/>
<apply>
<plus/>
<ci>v_R_2_sGC</ci>
<ci>v_R_3_sGC</ci>
</apply>
<ci>v_R_4_sGC</ci>
</apply>
</apply>
<apply>
<eq/>
<apply>
<diff/>
<bvar>
<ci>time</ci>
</bvar>
<ci>q_cGMP</ci>
</apply>
<apply>
<times/>
<apply>
<minus/>
<cn cellml:units="dimensionless">2</cn>
</apply>
<ci>v_R_4_sGC</ci>
</apply>
</apply>
<apply>
<eq/>
<apply>
<diff/>
<bvar>
<ci>time</ci>
</bvar>
<ci>q_NO_product</ci>
</apply>
<ci>v_R_DNO_sGC</ci>
</apply>
</math>
</component>
<component name="sGC_parameters">
<variable initial_value="996545" name="kappa_R_1_sGC" public_interface="out" units="fmol_per_sec"/>
<variable initial_value="0.00090595" name="kappa_R_2_sGC" public_interface="out" units="fmol_per_sec"/>
<variable initial_value="3.20816" name="kappa_R_3_sGC" public_interface="out" units="fmol_per_sec"/>
<variable initial_value="0.00996545" name="kappa_R_4_sGC" public_interface="out" units="fmol_per_sec"/>
<variable initial_value="0.0236081" name="kappa_R_DNO_sGC" public_interface="out" units="fmol_per_sec"/>
<variable initial_value="0.0638542" name="K_Eb" public_interface="out" units="per_fmol"/>
<variable initial_value="0.114174" name="K_NO" public_interface="out" units="per_fmol"/>
<variable initial_value="29.7524" name="K_E6c" public_interface="out" units="per_fmol"/>
<variable initial_value="0.297524" name="K_E5c" public_interface="out" units="per_fmol"/>
<variable initial_value="0.269542" name="K_cGMP" public_interface="out" units="per_fmol"/>
<variable initial_value="0.0114174" name="K_NO_product" public_interface="out" units="per_fmol"/>
</component>
<component name="sGC">
<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_R_1_sGC" public_interface="in" units="fmol_per_sec"/>
<variable name="kappa_R_2_sGC" public_interface="in" units="fmol_per_sec"/>
<variable name="kappa_R_3_sGC" public_interface="in" units="fmol_per_sec"/>
<variable name="kappa_R_4_sGC" public_interface="in" units="fmol_per_sec"/>
<variable name="kappa_R_DNO_sGC" public_interface="in" units="fmol_per_sec"/>
<variable name="K_Eb" public_interface="in" units="per_fmol"/>
<variable name="K_NO" public_interface="in" units="per_fmol"/>
<variable name="K_E6c" public_interface="in" units="per_fmol"/>
<variable name="K_E5c" public_interface="in" units="per_fmol"/>
<variable name="K_cGMP" public_interface="in" units="per_fmol"/>
<variable name="K_NO_product" public_interface="in" units="per_fmol"/>
<!-- Input from global environment-->
<variable name="q_Eb" public_interface="in" units="fmol"/>
<variable name="q_NO" public_interface="in" units="fmol"/>
<variable name="q_E6c" public_interface="in" units="fmol"/>
<variable name="q_E5c" public_interface="in" units="fmol"/>
<variable name="q_cGMP" public_interface="in" units="fmol"/>
<variable name="q_NO_product" public_interface="in" units="fmol"/>
<!-- Constitutive parameters-->
<variable name="mu_Eb" units="J_per_mol"/>
<variable name="mu_NO" units="J_per_mol"/>
<variable name="mu_E6c" units="J_per_mol"/>
<variable name="mu_E5c" units="J_per_mol"/>
<variable name="mu_cGMP" units="J_per_mol"/>
<variable name="mu_NO_product" units="J_per_mol"/>
<variable name="v_R_1_sGC" public_interface="out" units="fmol_per_sec"/>
<variable name="v_R_2_sGC" public_interface="out" units="fmol_per_sec"/>
<variable name="v_R_3_sGC" public_interface="out" units="fmol_per_sec"/>
<variable name="v_R_4_sGC" public_interface="out" units="fmol_per_sec"/>
<variable name="v_R_DNO_sGC" public_interface="out" units="fmol_per_sec"/>
<math xmlns="http://www.w3.org/1998/Math/MathML">
<apply>
<eq/>
<ci>mu_Eb</ci>
<apply>
<times/>
<ci>R</ci>
<ci>T</ci>
<apply>
<ln/>
<apply>
<times/>
<ci>K_Eb</ci>
<ci>q_Eb</ci>
</apply>
</apply>
</apply>
</apply>
<apply>
<eq/>
<ci>mu_NO</ci>
<apply>
<times/>
<ci>R</ci>
<ci>T</ci>
<apply>
<ln/>
<apply>
<times/>
<ci>K_NO</ci>
<ci>q_NO</ci>
</apply>
</apply>
</apply>
</apply>
<apply>
<eq/>
<ci>mu_E6c</ci>
<apply>
<times/>
<ci>R</ci>
<ci>T</ci>
<apply>
<ln/>
<apply>
<times/>
<ci>K_E6c</ci>
<ci>q_E6c</ci>
</apply>
</apply>
</apply>
</apply>
<apply>
<eq/>
<ci>mu_E5c</ci>
<apply>
<times/>
<ci>R</ci>
<ci>T</ci>
<apply>
<ln/>
<apply>
<times/>
<ci>K_E5c</ci>
<ci>q_E5c</ci>
</apply>
</apply>
</apply>
</apply>
<apply>
<eq/>
<ci>mu_cGMP</ci>
<apply>
<times/>
<ci>R</ci>
<ci>T</ci>
<apply>
<ln/>
<apply>
<times/>
<ci>K_cGMP</ci>
<ci>q_cGMP</ci>
</apply>
</apply>
</apply>
</apply>
<apply>
<eq/>
<ci>mu_NO_product</ci>
<apply>
<times/>
<ci>R</ci>
<ci>T</ci>
<apply>
<ln/>
<apply>
<times/>
<ci>K_NO_product</ci>
<ci>q_NO_product</ci>
</apply>
</apply>
</apply>
</apply>
<apply>
<eq/>
<ci>v_R_1_sGC</ci>
<apply>
<times/>
<ci>kappa_R_1_sGC</ci>
<apply>
<minus/>
<apply>
<exp/>
<apply>
<divide/>
<apply>
<plus/>
<ci>mu_Eb</ci>
<ci>mu_NO</ci>
</apply>
<apply>
<times/>
<ci>R</ci>
<ci>T</ci>
</apply>
</apply>
</apply>
<apply>
<exp/>
<apply>
<divide/>
<ci>mu_E6c</ci>
<apply>
<times/>
<ci>R</ci>
<ci>T</ci>
</apply>
</apply>
</apply>
</apply>
</apply>
</apply>
<apply>
<eq/>
<ci>v_R_2_sGC</ci>
<apply>
<times/>
<ci>kappa_R_2_sGC</ci>
<apply>
<minus/>
<apply>
<exp/>
<apply>
<divide/>
<ci>mu_E6c</ci>
<apply>
<times/>
<ci>R</ci>
<ci>T</ci>
</apply>
</apply>
</apply>
<apply>
<exp/>
<apply>
<divide/>
<ci>mu_E5c</ci>
<apply>
<times/>
<ci>R</ci>
<ci>T</ci>
</apply>
</apply>
</apply>
</apply>
</apply>
</apply>
<apply>
<eq/>
<ci>v_R_3_sGC</ci>
<apply>
<times/>
<ci>kappa_R_3_sGC</ci>
<apply>
<minus/>
<apply>
<exp/>
<apply>
<divide/>
<apply>
<plus/>
<ci>mu_E6c</ci>
<ci>mu_NO</ci>
</apply>
<apply>
<times/>
<ci>R</ci>
<ci>T</ci>
</apply>
</apply>
</apply>
<apply>
<exp/>
<apply>
<divide/>
<apply>
<plus/>
<ci>mu_E5c</ci>
<ci>mu_NO</ci>
</apply>
<apply>
<times/>
<ci>R</ci>
<ci>T</ci>
</apply>
</apply>
</apply>
</apply>
</apply>
</apply>
<apply>
<eq/>
<ci>v_R_4_sGC</ci>
<apply>
<times/>
<ci>kappa_R_4_sGC</ci>
<apply>
<minus/>
<apply>
<exp/>
<apply>
<divide/>
<apply>
<plus/>
<ci>mu_E5c</ci>
<apply>
<times/>
<ci>mu_cGMP</ci>
<cn cellml:units="dimensionless">2</cn>
</apply>
</apply>
<apply>
<times/>
<ci>R</ci>
<ci>T</ci>
</apply>
</apply>
</apply>
<apply>
<exp/>
<apply>
<divide/>
<apply>
<plus/>
<ci>mu_Eb</ci>
<ci>mu_NO</ci>
</apply>
<apply>
<times/>
<ci>R</ci>
<ci>T</ci>
</apply>
</apply>
</apply>
</apply>
</apply>
</apply>
<apply>
<eq/>
<ci>v_R_DNO_sGC</ci>
<apply>
<times/>
<ci>kappa_R_DNO_sGC</ci>
<apply>
<minus/>
<apply>
<exp/>
<apply>
<divide/>
<ci>mu_NO</ci>
<apply>
<times/>
<ci>R</ci>
<ci>T</ci>
</apply>
</apply>
</apply>
<apply>
<exp/>
<apply>
<divide/>
<ci>mu_NO_product</ci>
<apply>
<times/>
<ci>R</ci>
<ci>T</ci>
</apply>
</apply>
</apply>
</apply>
</apply>
</apply>
</math>
</component>
<connection>
<map_components component_1="environment" component_2="sGC"/>
<map_variables variable_1="time" variable_2="time"/>
<map_variables variable_1="q_Eb" variable_2="q_Eb"/>
<map_variables variable_1="q_NO" variable_2="q_NO"/>
<map_variables variable_1="q_E6c" variable_2="q_E6c"/>
<map_variables variable_1="q_E5c" variable_2="q_E5c"/>
<map_variables variable_1="q_cGMP" variable_2="q_cGMP"/>
<map_variables variable_1="q_NO_product" variable_2="q_NO_product"/>
<map_variables variable_1="v_R_1_sGC" variable_2="v_R_1_sGC"/>
<map_variables variable_1="v_R_2_sGC" variable_2="v_R_2_sGC"/>
<map_variables variable_1="v_R_3_sGC" variable_2="v_R_3_sGC"/>
<map_variables variable_1="v_R_4_sGC" variable_2="v_R_4_sGC"/>
<map_variables variable_1="v_R_DNO_sGC" variable_2="v_R_DNO_sGC"/>
</connection>
<connection>
<map_components component_1="sGC" component_2="sGC_parameters"/>
<map_variables variable_1="kappa_R_1_sGC" variable_2="kappa_R_1_sGC"/>
<map_variables variable_1="kappa_R_2_sGC" variable_2="kappa_R_2_sGC"/>
<map_variables variable_1="kappa_R_3_sGC" variable_2="kappa_R_3_sGC"/>
<map_variables variable_1="kappa_R_4_sGC" variable_2="kappa_R_4_sGC"/>
<map_variables variable_1="kappa_R_DNO_sGC" variable_2="kappa_R_DNO_sGC"/>
<map_variables variable_1="K_Eb" variable_2="K_Eb"/>
<map_variables variable_1="K_NO" variable_2="K_NO"/>
<map_variables variable_1="K_E6c" variable_2="K_E6c"/>
<map_variables variable_1="K_E5c" variable_2="K_E5c"/>
<map_variables variable_1="K_cGMP" variable_2="K_cGMP"/>
<map_variables variable_1="K_NO_product" variable_2="K_NO_product"/>
</connection>
<connection>
<map_components component_1="constants" component_2="sGC"/>
<map_variables variable_1="R" variable_2="R"/>
<map_variables variable_1="T" variable_2="T"/>
</connection>
</model>
