- Author:
- Shelley Fong <sfon036@UoA.auckland.ac.nz>
- Date:
- 2022-05-13 13:42:24+12:00
- Desc:
- forgot to update forward matrix
- Permanent Source URI:
- https://models.physiomeproject.org/workspace/856/rawfile/6a4e3e640452c398c30d4a60e8d041cc8896c6bd/BG_cGMP.cellml
<?xml version='1.0' encoding='UTF-8'?>
<model name="individual_cGMP" 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_GTP" 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_PDE" public_interface="out" units="fmol"/>
<variable initial_value="1e-18" name="q_GTP_E5c" public_interface="out" units="fmol"/>
<variable initial_value="1e-18" name="q_cGMP_PDE" public_interface="out" units="fmol"/>
<variable initial_value="1e-18" name="q_GMP" public_interface="out" units="fmol"/>
<!-- From submodule-->
<variable name="v_R_1a_cGMP" public_interface="in" units="fmol_per_sec"/>
<variable name="v_R_1b_cGMP" public_interface="in" units="fmol_per_sec"/>
<variable name="v_R_2a_cGMP" public_interface="in" units="fmol_per_sec"/>
<variable name="v_R_2b_cGMP" 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_GTP</ci>
</apply>
<apply>
<minus/>
<ci>v_R_1a_cGMP</ci>
</apply>
</apply>
<apply>
<eq/>
<apply>
<diff/>
<bvar>
<ci>time</ci>
</bvar>
<ci>q_E5c</ci>
</apply>
<apply>
<plus/>
<apply>
<minus/>
<ci>v_R_1a_cGMP</ci>
</apply>
<ci>v_R_1b_cGMP</ci>
</apply>
</apply>
<apply>
<eq/>
<apply>
<diff/>
<bvar>
<ci>time</ci>
</bvar>
<ci>q_cGMP</ci>
</apply>
<apply>
<minus/>
<apply>
<minus/>
<ci>v_R_1b_cGMP</ci>
<ci>v_R_2a_cGMP</ci>
</apply>
<ci>v_R_2b_cGMP</ci>
</apply>
</apply>
<apply>
<eq/>
<apply>
<diff/>
<bvar>
<ci>time</ci>
</bvar>
<ci>q_PDE</ci>
</apply>
<apply>
<plus/>
<apply>
<minus/>
<ci>v_R_2a_cGMP</ci>
</apply>
<ci>v_R_2b_cGMP</ci>
</apply>
</apply>
<apply>
<eq/>
<apply>
<diff/>
<bvar>
<ci>time</ci>
</bvar>
<ci>q_GTP_E5c</ci>
</apply>
<apply>
<minus/>
<ci>v_R_1a_cGMP</ci>
<ci>v_R_1b_cGMP</ci>
</apply>
</apply>
<apply>
<eq/>
<apply>
<diff/>
<bvar>
<ci>time</ci>
</bvar>
<ci>q_cGMP_PDE</ci>
</apply>
<apply>
<minus/>
<ci>v_R_2a_cGMP</ci>
<ci>v_R_2b_cGMP</ci>
</apply>
</apply>
<apply>
<eq/>
<apply>
<diff/>
<bvar>
<ci>time</ci>
</bvar>
<ci>q_GMP</ci>
</apply>
<ci>v_R_2b_cGMP</ci>
</apply>
</math>
</component>
<component name="cGMP_parameters">
<variable initial_value="1526.2" name="kappa_R_1a_cGMP" public_interface="out" units="fmol_per_sec"/>
<variable initial_value="0.0260064" name="kappa_R_1b_cGMP" public_interface="out" units="fmol_per_sec"/>
<variable initial_value="56591.2" name="kappa_R_2a_cGMP" public_interface="out" units="fmol_per_sec"/>
<variable initial_value="0.0173847" name="kappa_R_2b_cGMP" public_interface="out" units="fmol_per_sec"/>
<variable initial_value="2915.5" name="K_GTP" public_interface="out" units="per_fmol"/>
<variable initial_value="0.0163278" name="K_E5c" public_interface="out" units="per_fmol"/>
<variable initial_value="0.171097" name="K_cGMP" public_interface="out" units="per_fmol"/>
<variable initial_value="7.50344" name="K_PDE" public_interface="out" units="per_fmol"/>
<variable initial_value="176.61" name="K_GTP_E5c" public_interface="out" units="per_fmol"/>
<variable initial_value="9.52593" name="K_cGMP_PDE" public_interface="out" units="per_fmol"/>
<variable initial_value="0.000556962" name="K_GMP" public_interface="out" units="per_fmol"/>
</component>
<component name="cGMP">
<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_1a_cGMP" public_interface="in" units="fmol_per_sec"/>
<variable name="kappa_R_1b_cGMP" public_interface="in" units="fmol_per_sec"/>
<variable name="kappa_R_2a_cGMP" public_interface="in" units="fmol_per_sec"/>
<variable name="kappa_R_2b_cGMP" public_interface="in" units="fmol_per_sec"/>
<variable name="K_GTP" 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_PDE" public_interface="in" units="per_fmol"/>
<variable name="K_GTP_E5c" public_interface="in" units="per_fmol"/>
<variable name="K_cGMP_PDE" public_interface="in" units="per_fmol"/>
<variable name="K_GMP" public_interface="in" units="per_fmol"/>
<!-- Input from global environment-->
<variable name="q_GTP" 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_PDE" public_interface="in" units="fmol"/>
<variable name="q_GTP_E5c" public_interface="in" units="fmol"/>
<variable name="q_cGMP_PDE" public_interface="in" units="fmol"/>
<variable name="q_GMP" public_interface="in" units="fmol"/>
<!-- Constitutive parameters-->
<variable name="mu_GTP" units="J_per_mol"/>
<variable name="mu_E5c" units="J_per_mol"/>
<variable name="mu_cGMP" units="J_per_mol"/>
<variable name="mu_PDE" units="J_per_mol"/>
<variable name="mu_GTP_E5c" units="J_per_mol"/>
<variable name="mu_cGMP_PDE" units="J_per_mol"/>
<variable name="mu_GMP" units="J_per_mol"/>
<variable name="v_R_1a_cGMP" public_interface="out" units="fmol_per_sec"/>
<variable name="v_R_1b_cGMP" public_interface="out" units="fmol_per_sec"/>
<variable name="v_R_2a_cGMP" public_interface="out" units="fmol_per_sec"/>
<variable name="v_R_2b_cGMP" public_interface="out" units="fmol_per_sec"/>
<math xmlns="http://www.w3.org/1998/Math/MathML">
<apply>
<eq/>
<ci>mu_GTP</ci>
<apply>
<times/>
<ci>R</ci>
<ci>T</ci>
<apply>
<ln/>
<apply>
<times/>
<ci>K_GTP</ci>
<ci>q_GTP</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_PDE</ci>
<apply>
<times/>
<ci>R</ci>
<ci>T</ci>
<apply>
<ln/>
<apply>
<times/>
<ci>K_PDE</ci>
<ci>q_PDE</ci>
</apply>
</apply>
</apply>
</apply>
<apply>
<eq/>
<ci>mu_GTP_E5c</ci>
<apply>
<times/>
<ci>R</ci>
<ci>T</ci>
<apply>
<ln/>
<apply>
<times/>
<ci>K_GTP_E5c</ci>
<ci>q_GTP_E5c</ci>
</apply>
</apply>
</apply>
</apply>
<apply>
<eq/>
<ci>mu_cGMP_PDE</ci>
<apply>
<times/>
<ci>R</ci>
<ci>T</ci>
<apply>
<ln/>
<apply>
<times/>
<ci>K_cGMP_PDE</ci>
<ci>q_cGMP_PDE</ci>
</apply>
</apply>
</apply>
</apply>
<apply>
<eq/>
<ci>mu_GMP</ci>
<apply>
<times/>
<ci>R</ci>
<ci>T</ci>
<apply>
<ln/>
<apply>
<times/>
<ci>K_GMP</ci>
<ci>q_GMP</ci>
</apply>
</apply>
</apply>
</apply>
<apply>
<eq/>
<ci>v_R_1a_cGMP</ci>
<apply>
<times/>
<ci>kappa_R_1a_cGMP</ci>
<apply>
<minus/>
<apply>
<exp/>
<apply>
<divide/>
<apply>
<plus/>
<ci>mu_GTP</ci>
<ci>mu_E5c</ci>
</apply>
<apply>
<times/>
<ci>R</ci>
<ci>T</ci>
</apply>
</apply>
</apply>
<apply>
<exp/>
<apply>
<divide/>
<ci>mu_GTP_E5c</ci>
<apply>
<times/>
<ci>R</ci>
<ci>T</ci>
</apply>
</apply>
</apply>
</apply>
</apply>
</apply>
<apply>
<eq/>
<ci>v_R_1b_cGMP</ci>
<apply>
<times/>
<ci>kappa_R_1b_cGMP</ci>
<apply>
<minus/>
<apply>
<exp/>
<apply>
<divide/>
<ci>mu_GTP_E5c</ci>
<apply>
<times/>
<ci>R</ci>
<ci>T</ci>
</apply>
</apply>
</apply>
<apply>
<exp/>
<apply>
<divide/>
<apply>
<plus/>
<ci>mu_cGMP</ci>
<ci>mu_E5c</ci>
</apply>
<apply>
<times/>
<ci>R</ci>
<ci>T</ci>
</apply>
</apply>
</apply>
</apply>
</apply>
</apply>
<apply>
<eq/>
<ci>v_R_2a_cGMP</ci>
<apply>
<times/>
<ci>kappa_R_2a_cGMP</ci>
<apply>
<minus/>
<apply>
<exp/>
<apply>
<divide/>
<apply>
<plus/>
<ci>mu_cGMP</ci>
<ci>mu_PDE</ci>
</apply>
<apply>
<times/>
<ci>R</ci>
<ci>T</ci>
</apply>
</apply>
</apply>
<apply>
<exp/>
<apply>
<divide/>
<ci>mu_cGMP_PDE</ci>
<apply>
<times/>
<ci>R</ci>
<ci>T</ci>
</apply>
</apply>
</apply>
</apply>
</apply>
</apply>
<apply>
<eq/>
<ci>v_R_2b_cGMP</ci>
<apply>
<times/>
<ci>kappa_R_2b_cGMP</ci>
<apply>
<minus/>
<apply>
<exp/>
<apply>
<divide/>
<apply>
<plus/>
<ci>mu_cGMP_PDE</ci>
<ci>mu_cGMP</ci>
</apply>
<apply>
<times/>
<ci>R</ci>
<ci>T</ci>
</apply>
</apply>
</apply>
<apply>
<exp/>
<apply>
<divide/>
<apply>
<plus/>
<ci>mu_GMP</ci>
<ci>mu_PDE</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="cGMP"/>
<map_variables variable_1="time" variable_2="time"/>
<map_variables variable_1="q_GTP" variable_2="q_GTP"/>
<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_PDE" variable_2="q_PDE"/>
<map_variables variable_1="q_GTP_E5c" variable_2="q_GTP_E5c"/>
<map_variables variable_1="q_cGMP_PDE" variable_2="q_cGMP_PDE"/>
<map_variables variable_1="q_GMP" variable_2="q_GMP"/>
<map_variables variable_1="v_R_1a_cGMP" variable_2="v_R_1a_cGMP"/>
<map_variables variable_1="v_R_1b_cGMP" variable_2="v_R_1b_cGMP"/>
<map_variables variable_1="v_R_2a_cGMP" variable_2="v_R_2a_cGMP"/>
<map_variables variable_1="v_R_2b_cGMP" variable_2="v_R_2b_cGMP"/>
</connection>
<connection>
<map_components component_1="cGMP" component_2="cGMP_parameters"/>
<map_variables variable_1="kappa_R_1a_cGMP" variable_2="kappa_R_1a_cGMP"/>
<map_variables variable_1="kappa_R_1b_cGMP" variable_2="kappa_R_1b_cGMP"/>
<map_variables variable_1="kappa_R_2a_cGMP" variable_2="kappa_R_2a_cGMP"/>
<map_variables variable_1="kappa_R_2b_cGMP" variable_2="kappa_R_2b_cGMP"/>
<map_variables variable_1="K_GTP" variable_2="K_GTP"/>
<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_PDE" variable_2="K_PDE"/>
<map_variables variable_1="K_GTP_E5c" variable_2="K_GTP_E5c"/>
<map_variables variable_1="K_cGMP_PDE" variable_2="K_cGMP_PDE"/>
<map_variables variable_1="K_GMP" variable_2="K_GMP"/>
</connection>
<connection>
<map_components component_1="constants" component_2="cGMP"/>
<map_variables variable_1="R" variable_2="R"/>
<map_variables variable_1="T" variable_2="T"/>
</connection>
</model>
